From 7f0f3679481a9bc465360f0138f33a6bbe39e1f6 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Fri, 14 Jun 2024 14:29:27 +0100 Subject: [PATCH 01/47] add numpy 2 hotfix to main --- main.py | 58 ++++++++++++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 49 insertions(+), 9 deletions(-) diff --git a/main.py b/main.py index a6f9f1d..80beca5 100644 --- a/main.py +++ b/main.py @@ -260,6 +260,44 @@ "_anaconda_depends", ] +def _update_numpy_base_dependencies(fn, record, instructions): + depends = record.get("depends", []) + updated = False + for i, dep in enumerate(depends): + if dep.startswith("numpy-base") and '==' not in dep and '<' not in dep: + depends[i] = dep + ",<2.0a0" + updated = True + elif dep == "numpy-base": + depends[i] = "numpy-base <2.0a0" + updated = True + + if updated: + instructions["packages"][fn]['depends'] = depends + + return updated + +def _update_numpy_dependencies(fn, record, instructions): + depends = record.get("depends", []) + updated = False + for i, dep in enumerate(depends): + if dep.startswith("numpy"): + # If there's no upper bound and the dependency isn't pinned to a specific version + if '==' not in dep and '<' not in dep: + depends[i] = dep + ",<2.0a0" + updated = True + elif dep == "numpy": + depends[i] = "numpy <2.0a0" + updated = True + # Add an upper bound if it is missing in the dependency constraint + elif '==' not in dep and '<' not in dep: + depends[i] = dep + ",<2.0a0" + updated = True + + if updated: + instructions["packages"][fn]['depends'] = depends + + return updated + def _replace_vc_features_with_vc_pkg_deps(name, record, depends): python_vc_deps = { @@ -661,15 +699,17 @@ def patch_record_in_place(fn, record, subdir): # numpy # ######### - # Correct packages mistakenly built against 1.21.5 on linux-aarch64 - # Replaces the dependency bound with 1.21.2. These packages should - # actually have been built against an even earlier version of numpy. - # This is the safest correction we can make for now - if subdir == "linux-aarch64": - for i, dep in enumerate(depends): - if dep.startswith("numpy >=1.21.5,"): - depends[i] = depends[i].replace(">=1.21.5,", ">=1.21.2,") - break + # to update dependencies for preperation for numpy 2.0.0 + numpy_instructions = { + "patch_instructions_version": 1, + "packages": defaultdict(dict), + "revoke": [], + "remove": [], + } + if name == "numpy": + _update_numpy_dependencies(fn, record, numpy_instructions) + elif name == "numpy-base": + _update_numpy_base_dependencies(fn, record, numpy_instructions) ########### # pytorch # From 39ec561e9eb03af38c69d7950c214c08a2053c22 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Fri, 14 Jun 2024 16:50:24 +0100 Subject: [PATCH 02/47] ensure the lint passes --- main.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/main.py b/main.py index 80beca5..564b98c 100644 --- a/main.py +++ b/main.py @@ -260,6 +260,7 @@ "_anaconda_depends", ] + def _update_numpy_base_dependencies(fn, record, instructions): depends = record.get("depends", []) updated = False @@ -270,12 +271,11 @@ def _update_numpy_base_dependencies(fn, record, instructions): elif dep == "numpy-base": depends[i] = "numpy-base <2.0a0" updated = True - if updated: instructions["packages"][fn]['depends'] = depends - return updated + def _update_numpy_dependencies(fn, record, instructions): depends = record.get("depends", []) updated = False @@ -292,10 +292,8 @@ def _update_numpy_dependencies(fn, record, instructions): elif '==' not in dep and '<' not in dep: depends[i] = dep + ",<2.0a0" updated = True - if updated: instructions["packages"][fn]['depends'] = depends - return updated From 013d769398da7f7b14719fd55e528cba0a6bfac7 Mon Sep 17 00:00:00 2001 From: James Robertson Date: Tue, 18 Jun 2024 11:07:40 +0100 Subject: [PATCH 03/47] Apply suggestions from code review Co-authored-by: Charles Bousseau <16641587+cbouss@users.noreply.github.com> --- main.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/main.py b/main.py index 564b98c..f496d00 100644 --- a/main.py +++ b/main.py @@ -265,10 +265,10 @@ def _update_numpy_base_dependencies(fn, record, instructions): depends = record.get("depends", []) updated = False for i, dep in enumerate(depends): - if dep.startswith("numpy-base") and '==' not in dep and '<' not in dep: + if dep.split()[0] == "numpy-base" and '==' not in dep and '<' not in dep: depends[i] = dep + ",<2.0a0" updated = True - elif dep == "numpy-base": + else: depends[i] = "numpy-base <2.0a0" updated = True if updated: @@ -280,7 +280,7 @@ def _update_numpy_dependencies(fn, record, instructions): depends = record.get("depends", []) updated = False for i, dep in enumerate(depends): - if dep.startswith("numpy"): + if dep.split()[0] == "numpy": # If there's no upper bound and the dependency isn't pinned to a specific version if '==' not in dep and '<' not in dep: depends[i] = dep + ",<2.0a0" From b011dccf5cfb63c9326f87e7659902b134d07b68 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 18 Jun 2024 12:09:14 +0100 Subject: [PATCH 04/47] re-add numpy old hotfix --- main.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/main.py b/main.py index f496d00..2ef352f 100644 --- a/main.py +++ b/main.py @@ -697,6 +697,16 @@ def patch_record_in_place(fn, record, subdir): # numpy # ######### + # Correct packages mistakenly built against 1.21.5 on linux-aarch64 + # Replaces the dependency bound with 1.21.2. These packages should + # actually have been built against an even earlier version of numpy. + # This is the safest correction we can make for now + if subdir == "linux-aarch64": + for i, dep in enumerate(depends): + if dep.startswith("numpy >=1.21.5,"): + depends[i] = depends[i].replace(">=1.21.5,", ">=1.21.2,") + break + # to update dependencies for preperation for numpy 2.0.0 numpy_instructions = { "patch_instructions_version": 1, From e38027f41fa401d944138ae9a3a2d6689feceb62 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 18 Jun 2024 12:18:06 +0100 Subject: [PATCH 05/47] ensure find packages with lock without == --- main.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/main.py b/main.py index 2ef352f..6cba597 100644 --- a/main.py +++ b/main.py @@ -282,16 +282,12 @@ def _update_numpy_dependencies(fn, record, instructions): for i, dep in enumerate(depends): if dep.split()[0] == "numpy": # If there's no upper bound and the dependency isn't pinned to a specific version - if '==' not in dep and '<' not in dep: + if '==' not in dep and "1." not in dep and '<' not in dep: depends[i] = dep + ",<2.0a0" updated = True elif dep == "numpy": depends[i] = "numpy <2.0a0" updated = True - # Add an upper bound if it is missing in the dependency constraint - elif '==' not in dep and '<' not in dep: - depends[i] = dep + ",<2.0a0" - updated = True if updated: instructions["packages"][fn]['depends'] = depends return updated From 67417d8866368521bc83e45b148bb2775c38f0f8 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 18 Jun 2024 14:09:41 +0100 Subject: [PATCH 06/47] propogate find changes to be made --- main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.py b/main.py index 6cba597..f77d4db 100644 --- a/main.py +++ b/main.py @@ -265,7 +265,7 @@ def _update_numpy_base_dependencies(fn, record, instructions): depends = record.get("depends", []) updated = False for i, dep in enumerate(depends): - if dep.split()[0] == "numpy-base" and '==' not in dep and '<' not in dep: + if dep.split()[0] == "numpy-base" and '==' not in dep and "1." not in dep and '<' not in dep: depends[i] = dep + ",<2.0a0" updated = True else: From 0a93cab4d55e0281baf1bfdb15c40ce510903e31 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Wed, 19 Jun 2024 09:12:43 +0100 Subject: [PATCH 07/47] ensure correct application of upper bound hotfix --- main.py | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/main.py b/main.py index f77d4db..93e1ae0 100644 --- a/main.py +++ b/main.py @@ -265,12 +265,12 @@ def _update_numpy_base_dependencies(fn, record, instructions): depends = record.get("depends", []) updated = False for i, dep in enumerate(depends): + if dep.split()[0] == "numpy-base": + depends[i] = "numpy-base <2.0a0" + updated = True if dep.split()[0] == "numpy-base" and '==' not in dep and "1." not in dep and '<' not in dep: depends[i] = dep + ",<2.0a0" updated = True - else: - depends[i] = "numpy-base <2.0a0" - updated = True if updated: instructions["packages"][fn]['depends'] = depends return updated @@ -282,12 +282,13 @@ def _update_numpy_dependencies(fn, record, instructions): for i, dep in enumerate(depends): if dep.split()[0] == "numpy": # If there's no upper bound and the dependency isn't pinned to a specific version - if '==' not in dep and "1." not in dep and '<' not in dep: - depends[i] = dep + ",<2.0a0" - updated = True - elif dep == "numpy": + if dep == "numpy": depends[i] = "numpy <2.0a0" updated = True + elif '==' not in dep and "1." not in dep and '<' not in dep: + depends[i] = dep + ",<2.0a0" + updated = True + if updated: instructions["packages"][fn]['depends'] = depends return updated @@ -710,10 +711,13 @@ def patch_record_in_place(fn, record, subdir): "revoke": [], "remove": [], } - if name == "numpy": - _update_numpy_dependencies(fn, record, numpy_instructions) - elif name == "numpy-base": - _update_numpy_base_dependencies(fn, record, numpy_instructions) + for i, dep in enumerate(depends): + if dep == "numpy": + print("Updating numpy dependencies for %s" % fn) + _update_numpy_dependencies(fn, record, numpy_instructions) + elif dep == "numpy-base": + print("Updating numpy-base dependencies for %s" % fn) + _update_numpy_base_dependencies(fn, record, numpy_instructions) ########### # pytorch # From d0d073ba6d112697f85cb0d0d0a370b1b35976f3 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Wed, 19 Jun 2024 15:36:58 +0100 Subject: [PATCH 08/47] avoid anaconda_depends for repin of numpy --- main.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/main.py b/main.py index 93e1ae0..68ee1fd 100644 --- a/main.py +++ b/main.py @@ -712,11 +712,9 @@ def patch_record_in_place(fn, record, subdir): "remove": [], } for i, dep in enumerate(depends): - if dep == "numpy": - print("Updating numpy dependencies for %s" % fn) + if dep == "numpy" and name != "_anaconda_depends": _update_numpy_dependencies(fn, record, numpy_instructions) - elif dep == "numpy-base": - print("Updating numpy-base dependencies for %s" % fn) + elif dep == "numpy-base" and name != "_anaconda_depends": _update_numpy_base_dependencies(fn, record, numpy_instructions) ########### From d35eab8259b849950f253a926b39a279a90363da Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 25 Jun 2024 17:55:50 +0100 Subject: [PATCH 09/47] add protection list and logic to the n2 hotfix --- main.py | 73 ++++++++++++++++++++++++++++----------------- numpy2_protect.yaml | 6 ++++ 2 files changed, 51 insertions(+), 28 deletions(-) create mode 100644 numpy2_protect.yaml diff --git a/main.py b/main.py index 68ee1fd..4cd2c9a 100644 --- a/main.py +++ b/main.py @@ -2,6 +2,7 @@ import copy import fnmatch import json +import yaml import os import re import sys @@ -260,35 +261,53 @@ "_anaconda_depends", ] +# Load the configuration file +with open('numpy2_protect.yaml', 'r') as f: + numpy2_protect_dict = yaml.safe_load(f) -def _update_numpy_base_dependencies(fn, record, instructions): - depends = record.get("depends", []) - updated = False - for i, dep in enumerate(depends): - if dep.split()[0] == "numpy-base": - depends[i] = "numpy-base <2.0a0" - updated = True - if dep.split()[0] == "numpy-base" and '==' not in dep and "1." not in dep and '<' not in dep: - depends[i] = dep + ",<2.0a0" - updated = True - if updated: - instructions["packages"][fn]['depends'] = depends - return updated +def parse_version(version_str): + # Extract the version number without any comparison operators + match = re.search(r'(\d+(\.\d+)*)', version_str) + return match.group(1) if match else None -def _update_numpy_dependencies(fn, record, instructions): +def has_upper_bound(dep): + # Check if the dependency string already contains an upper bound + return any(part.strip().startswith('<') for part in dep.split(',')) + +def has_comparison_operator(dep): + # Check if the dependency string contains a comparison operator + return any(op in dep for op in ['<', '>', '=']) + +def update_numpy_dependencies(fn, record, instructions): depends = record.get("depends", []) updated = False for i, dep in enumerate(depends): - if dep.split()[0] == "numpy": - # If there's no upper bound and the dependency isn't pinned to a specific version - if dep == "numpy": - depends[i] = "numpy <2.0a0" - updated = True - elif '==' not in dep and "1." not in dep and '<' not in dep: - depends[i] = dep + ",<2.0a0" - updated = True - + parts = dep.split() + pkg = parts[0] + if pkg in ["numpy", "numpy-base"]: + if not has_upper_bound(dep): + if pkg in numpy2_protect_dict: + version_str = parts[1] if len(parts) > 1 else None + version = parse_version(version_str) if version_str else None + protect_version = parse_version(numpy2_protect_dict[pkg]) + + if version and protect_version: + try: + if VersionOrder(version) <= VersionOrder(protect_version): + if has_comparison_operator(dep): + depends[i] = f"{dep},<2.0a0" + updated = True + except ValueError: + # If we can't compare versions, we'll add the bound to be safe + if has_comparison_operator(dep): + depends[i] = f"{dep},<2.0a0" + updated = True + # Only add bound if explicitly specified in config and no upper bound exists + elif numpy2_protect_dict.get('add_bound_to_unspecified', False): + if has_comparison_operator(dep): + depends[i] = f"{dep},<2.0a0" + updated = True if updated: instructions["packages"][fn]['depends'] = depends return updated @@ -711,12 +730,10 @@ def patch_record_in_place(fn, record, subdir): "revoke": [], "remove": [], } - for i, dep in enumerate(depends): - if dep == "numpy" and name != "_anaconda_depends": - _update_numpy_dependencies(fn, record, numpy_instructions) - elif dep == "numpy-base" and name != "_anaconda_depends": - _update_numpy_base_dependencies(fn, record, numpy_instructions) + for i, dep in enumerate(depends): + if dep.split()[0] in ["numpy", "numpy-base"] and name != "_anaconda_depends": + update_numpy_dependencies(fn, record, numpy_instructions) ########### # pytorch # ########### diff --git a/numpy2_protect.yaml b/numpy2_protect.yaml new file mode 100644 index 0000000..719fb85 --- /dev/null +++ b/numpy2_protect.yaml @@ -0,0 +1,6 @@ +add_bound_to_unspecified: true # Set to true if you want to add bounds to unlisted packages +numpy: '1.25.0' +numpy-base: '1.25.0' +pandas: '2.2.2' +scikit-learn: '1.4.2' +# Add more packages as needed \ No newline at end of file From 513846afaa453850f957ca962157f9501d7330a7 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 25 Jun 2024 17:59:17 +0100 Subject: [PATCH 10/47] lint issues --- main.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/main.py b/main.py index 4cd2c9a..61fc402 100644 --- a/main.py +++ b/main.py @@ -265,20 +265,22 @@ with open('numpy2_protect.yaml', 'r') as f: numpy2_protect_dict = yaml.safe_load(f) - def parse_version(version_str): # Extract the version number without any comparison operators match = re.search(r'(\d+(\.\d+)*)', version_str) return match.group(1) if match else None + def has_upper_bound(dep): # Check if the dependency string already contains an upper bound return any(part.strip().startswith('<') for part in dep.split(',')) + def has_comparison_operator(dep): # Check if the dependency string contains a comparison operator return any(op in dep for op in ['<', '>', '=']) + def update_numpy_dependencies(fn, record, instructions): depends = record.get("depends", []) updated = False @@ -291,7 +293,7 @@ def update_numpy_dependencies(fn, record, instructions): version_str = parts[1] if len(parts) > 1 else None version = parse_version(version_str) if version_str else None protect_version = parse_version(numpy2_protect_dict[pkg]) - + if version and protect_version: try: if VersionOrder(version) <= VersionOrder(protect_version): From 9e1ab7b0a1c955dbb0f672210bc8781c1ccb689e Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 25 Jun 2024 18:00:43 +0100 Subject: [PATCH 11/47] lint issue --- main.py | 1 + 1 file changed, 1 insertion(+) diff --git a/main.py b/main.py index 61fc402..fc7b131 100644 --- a/main.py +++ b/main.py @@ -265,6 +265,7 @@ with open('numpy2_protect.yaml', 'r') as f: numpy2_protect_dict = yaml.safe_load(f) + def parse_version(version_str): # Extract the version number without any comparison operators match = re.search(r'(\d+(\.\d+)*)', version_str) From b0fd63eb47acb4aab1648abf1e2bfb951ff3986d Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 25 Jun 2024 18:02:12 +0100 Subject: [PATCH 12/47] pyyaml added --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 543b677..ee43508 100644 --- a/Makefile +++ b/Makefile @@ -16,7 +16,7 @@ help: init: @if [ -z "$${CONDA_SHLVL:+x}" ]; then echo "Conda is not installed." && exit 1; fi - @conda create -y -n repodata-hotfixes conda conda-index flake8 pytest requests + @conda create -y -n repodata-hotfixes conda conda-index flake8 pytest requests pyyaml check: lint test From 71306c3f05c22aa6803c9d3e5fbaaf1984a9f29e Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 25 Jun 2024 18:04:24 +0100 Subject: [PATCH 13/47] pyyaml in testenv --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e56670d..136acbf 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,7 +19,7 @@ jobs: - name: Setup environment shell: bash -l {0} run: | - conda create --name testenv conda conda-index flake8 requests + conda create --name testenv conda conda-index flake8 requests pyyaml - name: Lint shell: bash -l {0} run: | From ce7e20be988e5d4d188617f8132f0fb012c325d3 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 16 Jul 2024 13:55:25 +0100 Subject: [PATCH 14/47] modify yaml and ensure upto date filtering of edge cases --- main.py | 164 +++++++++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 132 insertions(+), 32 deletions(-) diff --git a/main.py b/main.py index fc7b131..748a8ea 100644 --- a/main.py +++ b/main.py @@ -6,13 +6,25 @@ import os import re import sys +import datetime from collections import defaultdict from os.path import dirname, isdir, isfile, join - +import rattler +from typing import List, Dict, Any, Sequence, Optional from conda.models.version import VersionOrder import requests +import logging + +# Configure the logging +logging.basicConfig(level=logging.DEBUG, + format='%(asctime)s - %(name)s - %(levelname)s - %(message)s', + handlers=[logging.FileHandler('hotfixes.log', mode='w'), + logging.StreamHandler()]) +# Create a logger object +logger = logging.getLogger(__name__) + CHANNEL_NAME = "main" CHANNEL_ALIAS = "https://repo.anaconda.com/pkgs" SUBDIRS = ( @@ -265,6 +277,42 @@ with open('numpy2_protect.yaml', 'r') as f: numpy2_protect_dict = yaml.safe_load(f) +async def solve_dependencies( + record: rattler.RepoDataRecord, + channels: Sequence[rattler.Channel | str], + platforms: Sequence[rattler.Platform | rattler.platform.PlatformLiteral], + virtual_packages: Sequence[rattler.GenericVirtualPackage | rattler.VirtualPackage] +) -> List[rattler.RepoDataRecord]: + try: + # Create a MatchSpec for the current package + name = record.name.normalized + if name == '_anaconda_depends': + return [] + version = record.version._source + build = record.build + package_spec = rattler.MatchSpec(f"{name}={version}={build}") + + # Create MatchSpecs for all dependencies + dep_specs = [rattler.MatchSpec(dep) for dep in record.depends] + + # Combine the package spec and dependency specs + all_specs = [package_spec] + dep_specs + + # Solve dependencies + solved_packages = await rattler.solve( + channels=channels, + specs=all_specs, + platforms=platforms, + virtual_packages=virtual_packages, + timeout=datetime.timedelta(seconds=10), + strategy="highest" # You can adjust this if needed + ) + logger.info(f"Solved dependencies for {name}") + return solved_packages + except Exception as exc: + logger.error(f"Failed to solve dependencies for {name}: {exc}") + return [] + def parse_version(version_str): # Extract the version number without any comparison operators @@ -277,42 +325,72 @@ def has_upper_bound(dep): return any(part.strip().startswith('<') for part in dep.split(',')) -def has_comparison_operator(dep): - # Check if the dependency string contains a comparison operator - return any(op in dep for op in ['<', '>', '=']) +def patch_record_with_fixed_deps(dependency, parts): + # Fix the dependency string by adding an upper bound + # If it has a fixed value without == operator, leave it untouched + # If it has a fixed value with == operator, leave it untouched + # If it has a lower bound, add an upper bound + # If it has an upper bound, leave it untouched + + # Extract the version number without any comparison operators + version_str = parts[1] + version = parse_version(version_str) + if version: + if version_str.startswith('=='): + return dependency + if version_str.startswith('<'): + return dependency + if version_str.startswith('>') or version_str.startswith('>='): + dependency = f"{dependency},<2.0a0" + else: + dependency = f"{dependency} <2.0a0" -def update_numpy_dependencies(fn, record, instructions): - depends = record.get("depends", []) +def update_numpy_dependencies(dep_list, record, dep_type): updated = False - for i, dep in enumerate(depends): + non_update_logging = False + for i, dep in enumerate(dep_list): parts = dep.split() pkg = parts[0] if pkg in ["numpy", "numpy-base"]: + pkg_info = f"{record['name']} v{record['version']} (build: {record['build']}, build_number: {record['build_number']})" if not has_upper_bound(dep): if pkg in numpy2_protect_dict: version_str = parts[1] if len(parts) > 1 else None version = parse_version(version_str) if version_str else None protect_version = parse_version(numpy2_protect_dict[pkg]) - if version and protect_version: try: if VersionOrder(version) <= VersionOrder(protect_version): - if has_comparison_operator(dep): - depends[i] = f"{dep},<2.0a0" - updated = True - except ValueError: - # If we can't compare versions, we'll add the bound to be safe - if has_comparison_operator(dep): - depends[i] = f"{dep},<2.0a0" + dep_list[i] = f"{dep},<2.0a0" if len(parts) > 1 else f"{dep} <2.0a0" updated = True - # Only add bound if explicitly specified in config and no upper bound exists + logger.info(f"numpy 2.0.0: Updated {dep_type} for {pkg_info}. Original: '{dep}' -> New: '{dep_list[i]}' (Version <= protect_version)") + except ValueError: + dep_list[i] = f"{dep},<2.0a0" if len(parts) > 1 else f"{dep} <2.0a0" + updated = True + logger.info(f"numpy 2.0.0: Updated {dep_type} for {pkg_info}. Original: '{dep}' -> New: '{dep_list[i]}' (Version comparison failed)") + elif non_update_logging: + logger.info(f"numpy 2.0.0: No change to {dep_type} for {pkg_info}. Dependency: '{dep}' (Missing version or protect_version)") elif numpy2_protect_dict.get('add_bound_to_unspecified', False): - if has_comparison_operator(dep): - depends[i] = f"{dep},<2.0a0" - updated = True - if updated: - instructions["packages"][fn]['depends'] = depends + version_str = parts[1] if len(parts) > 1 else None + version = parse_version(version_str) if version_str else None + if version and non_update_logging: + logger.info(f"numpy 2.0.0: No change to {dep_type} for {pkg_info}. Dependency: '{dep}' (Version: {version})") + else: + if len(parts) > 1: + dependency = patch_record_with_fixed_deps(dep_list[i], parts) + if dependency: + dep_list[i] = dependency + updated = True + logger.info(f"numpy 2.0.0: Updated {dep_type} for {pkg_info}. Original: '{dep}' -> New: '{dep_list[i]}' (Unspecified bound added)") + else: + dep_list[i] = f"{dep} <2.0a0" + logger.info(f"numpy 2.0.0: Updated {dep_type} for {pkg_info}. Original: '{dep}' -> New: '{dep_list[i]}' (Unspecified bound added)") + elif non_update_logging: + logger.info(f"numpy 2.0.0: No change to {dep_type} for {pkg_info}. Dependency: '{dep}' (Not in protect_dict, no unspecified bound)") + elif non_update_logging: + logger.info(f"numpy 2.0.0: No change to {dep_type} for {pkg_info}. Dependency: '{dep}' (Already has upper bound)") + return updated @@ -514,6 +592,18 @@ def _fix_cudnn_depends(depends, subdir): idx = depends.index(original_cudnn_depend) depends[idx] = correct_cudnn_depends +def filter_packages(repo_data, substring): + + # Initialize the new dictionary to store filtered results + filtered_dict = {} + + # Loop through each key-value pair in the 'Packages' dictionary + for key, value in repo_data.items(): + # If the key contains the desired substring, add it to the filtered dictionary + if substring in key: + filtered_dict[key] = value + + return filtered_dict def _patch_repodata(repodata, subdir): index = repodata["packages"] @@ -726,17 +816,27 @@ def patch_record_in_place(fn, record, subdir): depends[i] = depends[i].replace(">=1.21.5,", ">=1.21.2,") break - # to update dependencies for preperation for numpy 2.0.0 - numpy_instructions = { - "patch_instructions_version": 1, - "packages": defaultdict(dict), - "revoke": [], - "remove": [], - } - - for i, dep in enumerate(depends): - if dep.split()[0] in ["numpy", "numpy-base"] and name != "_anaconda_depends": - update_numpy_dependencies(fn, record, numpy_instructions) + # To update dependencies for preperation for numpy 2.0.0 + # Do not patch packages depending on lower versions than 3.9 as there is no numpy2 for 3.8 and below. + # Do not patch packages depending on 3.13 and above as numpy2 will be the base version. + # TODO Verify noarch packages. + # TODO output as csv instead of logs for further analysis + # TODO simulate solves with rattler? https://github.com/anaconda/rbr-tooling/blob/main/scripts/multi-versions-stats.py + # TODO Identify edge cases. (Weird constraints...) + skip_log = False + if "py39" in fn or "py310" in fn or "py311" in fn or "py312" in fn: + if name not in ["anaconda", "_anaconda_depends"]: + for i, dep in enumerate(depends): + if dep.split()[0] in ["numpy", "numpy-base"]: + update_numpy_dependencies(depends, record, "dep") + elif skip_log: + logger.debug(f"numpy 2.0.0 skip {fn}") + for i, constrain in enumerate(constrains): + if constrain.split()[0] in ["numpy", "numpy-base"]: + update_numpy_dependencies(constrains, record, "constr") + break + elif skip_log: + logger.debug(f"numpy 2.0.0 skip {fn}") ########### # pytorch # ########### From 0863898baf78cf27ce7b4478ee5ce7a678c5786f Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 16 Jul 2024 14:00:35 +0100 Subject: [PATCH 15/47] remove need for yaml --- main.py | 8 ++------ numpy2_config.py | 6 ++++++ 2 files changed, 8 insertions(+), 6 deletions(-) create mode 100644 numpy2_config.py diff --git a/main.py b/main.py index 748a8ea..aa33d67 100644 --- a/main.py +++ b/main.py @@ -2,7 +2,6 @@ import copy import fnmatch import json -import yaml import os import re import sys @@ -12,8 +11,9 @@ import rattler from typing import List, Dict, Any, Sequence, Optional from conda.models.version import VersionOrder - +import csv import requests +from numpy2_config import numpy2_protect_dict import logging @@ -273,10 +273,6 @@ "_anaconda_depends", ] -# Load the configuration file -with open('numpy2_protect.yaml', 'r') as f: - numpy2_protect_dict = yaml.safe_load(f) - async def solve_dependencies( record: rattler.RepoDataRecord, channels: Sequence[rattler.Channel | str], diff --git a/numpy2_config.py b/numpy2_config.py new file mode 100644 index 0000000..686564b --- /dev/null +++ b/numpy2_config.py @@ -0,0 +1,6 @@ +numpy2_protect_dict = { + 'add_bound_to_unspecified': True, + 'pandas': '2.2.2', + 'scikit-learn': '1.4.2', + # Add more packages as needed +} \ No newline at end of file From c979b121ee9f0470d4a10c51c6feb5479c64e08d Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 16 Jul 2024 14:02:58 +0100 Subject: [PATCH 16/47] remove pyyaml --- .github/workflows/ci.yml | 2 +- Makefile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 136acbf..e56670d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,7 +19,7 @@ jobs: - name: Setup environment shell: bash -l {0} run: | - conda create --name testenv conda conda-index flake8 requests pyyaml + conda create --name testenv conda conda-index flake8 requests - name: Lint shell: bash -l {0} run: | diff --git a/Makefile b/Makefile index ee43508..543b677 100644 --- a/Makefile +++ b/Makefile @@ -16,7 +16,7 @@ help: init: @if [ -z "$${CONDA_SHLVL:+x}" ]; then echo "Conda is not installed." && exit 1; fi - @conda create -y -n repodata-hotfixes conda conda-index flake8 pytest requests pyyaml + @conda create -y -n repodata-hotfixes conda conda-index flake8 pytest requests check: lint test From 881cf7564fb04bce3604606adbc8d3dc50f39cab Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 25 Jul 2024 10:00:21 +0100 Subject: [PATCH 17/47] add numpy 2 hotfix rework --- main.py | 197 ++++++++++++++++++------------------- numpy2.py | 248 +++++++++++++++++++++++++++++++++++++++++++++++ numpy2_config.py | 2 + test_numpy.py | 90 +++++++++++++++++ 4 files changed, 437 insertions(+), 100 deletions(-) create mode 100644 numpy2.py create mode 100644 test_numpy.py diff --git a/main.py b/main.py index aa33d67..f3656dd 100644 --- a/main.py +++ b/main.py @@ -12,11 +12,15 @@ from typing import List, Dict, Any, Sequence, Optional from conda.models.version import VersionOrder import csv +from collections import defaultdict import requests from numpy2_config import numpy2_protect_dict import logging +# Global dictionary to store data for CSV output +csv_data = defaultdict(list) + # Configure the logging logging.basicConfig(level=logging.DEBUG, format='%(asctime)s - %(name)s - %(levelname)s - %(message)s', @@ -273,12 +277,86 @@ "_anaconda_depends", ] +def load_numpy_changes(): + try: + with open('proposed_numpy_changes.json', 'r') as f: + return json.load(f) + except FileNotFoundError: + logger.warning("proposed_numpy_changes.json not found. No numpy changes will be applied.") + return {} + +NUMPY_CHANGES = load_numpy_changes() + + +def apply_numpy_changes(record, subdir, filename): + """ + Applies predefined numpy changes to a record based on its directory and filename. + + Parameters: + - record: The record to update. + - subdir: The subdirectory of the record. + - filename: The filename of the record. + """ + if subdir not in NUMPY_CHANGES or filename not in NUMPY_CHANGES[subdir]: + return + + changes = NUMPY_CHANGES[subdir][filename] + for change in changes: + depends = _get_dependency_list(record, change['type']) + if depends is None: + continue + + _apply_changes_to_dependencies(depends, change, record, filename, 'type') + +def _get_dependency_list(record, change_type): + """ + Returns the appropriate dependency list based on the change type. + + Parameters: + - record (dict): The record containing dependency information. + - change_type (str): The type of change ('dep' for dependencies, 'constr' for constraints). + + Returns: + - list: The list of dependencies or constraints based on the change type, or None if the change type is unrecognized. + """ + if change_type == 'dep': + return record['depends'] + elif change_type == 'constr': + return record.get('constrains', []) + return None + +def _apply_changes_to_dependencies(depends, change, record, filename, sort_type='reason'): + """ + Applies changes to dependencies and logs the changes. + + Parameters: + - depends (list): The list of dependencies to be modified. + - change (dict): A dictionary containing the 'original' dependency, the 'updated' dependency, and the 'reason' for the change. + - record (dict): The record to which the changes apply. + - filename (str): The name of the file being processed. + - sort_type (str, optional): The key in the 'change' dictionary to sort the CSV data by. Defaults to 'reason'. + """ + for i, dep in enumerate(depends): + if dep == change['original']: + depends[i] = change['updated'] + if change['reason'] == 'Upper bound added': + logger.info(f"Applied numpy change for {filename}: {change['original']} -> {change['updated']}") + # Add to csv_data for later CSV export + csv_data[change[sort_type]].append([ + record['name'], record['version'], record['build'], + record['build_number'], change['original'], + change['updated'], change['reason'] + ]) + + async def solve_dependencies( record: rattler.RepoDataRecord, channels: Sequence[rattler.Channel | str], platforms: Sequence[rattler.Platform | rattler.platform.PlatformLiteral], virtual_packages: Sequence[rattler.GenericVirtualPackage | rattler.VirtualPackage] ) -> List[rattler.RepoDataRecord]: + # This is left in the file as it will be useful for future development + # and testing. It is not used in the current implementation. try: # Create a MatchSpec for the current package name = record.name.normalized @@ -310,84 +388,17 @@ async def solve_dependencies( return [] -def parse_version(version_str): - # Extract the version number without any comparison operators - match = re.search(r'(\d+(\.\d+)*)', version_str) - return match.group(1) if match else None - - -def has_upper_bound(dep): - # Check if the dependency string already contains an upper bound - return any(part.strip().startswith('<') for part in dep.split(',')) - - -def patch_record_with_fixed_deps(dependency, parts): - # Fix the dependency string by adding an upper bound - # If it has a fixed value without == operator, leave it untouched - # If it has a fixed value with == operator, leave it untouched - # If it has a lower bound, add an upper bound - # If it has an upper bound, leave it untouched - - # Extract the version number without any comparison operators - version_str = parts[1] - version = parse_version(version_str) - if version: - if version_str.startswith('=='): - return dependency - if version_str.startswith('<'): - return dependency - if version_str.startswith('>') or version_str.startswith('>='): - dependency = f"{dependency},<2.0a0" - else: - dependency = f"{dependency} <2.0a0" - - -def update_numpy_dependencies(dep_list, record, dep_type): - updated = False - non_update_logging = False - for i, dep in enumerate(dep_list): - parts = dep.split() - pkg = parts[0] - if pkg in ["numpy", "numpy-base"]: - pkg_info = f"{record['name']} v{record['version']} (build: {record['build']}, build_number: {record['build_number']})" - if not has_upper_bound(dep): - if pkg in numpy2_protect_dict: - version_str = parts[1] if len(parts) > 1 else None - version = parse_version(version_str) if version_str else None - protect_version = parse_version(numpy2_protect_dict[pkg]) - if version and protect_version: - try: - if VersionOrder(version) <= VersionOrder(protect_version): - dep_list[i] = f"{dep},<2.0a0" if len(parts) > 1 else f"{dep} <2.0a0" - updated = True - logger.info(f"numpy 2.0.0: Updated {dep_type} for {pkg_info}. Original: '{dep}' -> New: '{dep_list[i]}' (Version <= protect_version)") - except ValueError: - dep_list[i] = f"{dep},<2.0a0" if len(parts) > 1 else f"{dep} <2.0a0" - updated = True - logger.info(f"numpy 2.0.0: Updated {dep_type} for {pkg_info}. Original: '{dep}' -> New: '{dep_list[i]}' (Version comparison failed)") - elif non_update_logging: - logger.info(f"numpy 2.0.0: No change to {dep_type} for {pkg_info}. Dependency: '{dep}' (Missing version or protect_version)") - elif numpy2_protect_dict.get('add_bound_to_unspecified', False): - version_str = parts[1] if len(parts) > 1 else None - version = parse_version(version_str) if version_str else None - if version and non_update_logging: - logger.info(f"numpy 2.0.0: No change to {dep_type} for {pkg_info}. Dependency: '{dep}' (Version: {version})") - else: - if len(parts) > 1: - dependency = patch_record_with_fixed_deps(dep_list[i], parts) - if dependency: - dep_list[i] = dependency - updated = True - logger.info(f"numpy 2.0.0: Updated {dep_type} for {pkg_info}. Original: '{dep}' -> New: '{dep_list[i]}' (Unspecified bound added)") - else: - dep_list[i] = f"{dep} <2.0a0" - logger.info(f"numpy 2.0.0: Updated {dep_type} for {pkg_info}. Original: '{dep}' -> New: '{dep_list[i]}' (Unspecified bound added)") - elif non_update_logging: - logger.info(f"numpy 2.0.0: No change to {dep_type} for {pkg_info}. Dependency: '{dep}' (Not in protect_dict, no unspecified bound)") - elif non_update_logging: - logger.info(f"numpy 2.0.0: No change to {dep_type} for {pkg_info}. Dependency: '{dep}' (Already has upper bound)") +def write_csv(): + """ + Writes update data to CSV files in the 'updates' directory. + """ + if not os.path.exists("updates"): + os.makedirs("updates") - return updated + for issue_type, data in csv_data.items(): + with open(f"updates/{issue_type}_numpy2_updates.csv", 'w', newline='') as csvfile: + csv.writer(csvfile).writerow(['Package', 'Version', 'Build', 'Build Number', 'Original Dependency', 'Updated Dependency', 'Reason']) + csv.writer(csvfile).writerows(data) def _replace_vc_features_with_vc_pkg_deps(name, record, depends): @@ -689,6 +700,8 @@ def patch_record_in_place(fn, record, subdir): depends = record["depends"] constrains = record.get("constrains", []) + # depends = [dep for dep in depends if dep is not None] + ########## # subdir # ########## @@ -812,27 +825,9 @@ def patch_record_in_place(fn, record, subdir): depends[i] = depends[i].replace(">=1.21.5,", ">=1.21.2,") break - # To update dependencies for preperation for numpy 2.0.0 - # Do not patch packages depending on lower versions than 3.9 as there is no numpy2 for 3.8 and below. - # Do not patch packages depending on 3.13 and above as numpy2 will be the base version. - # TODO Verify noarch packages. - # TODO output as csv instead of logs for further analysis - # TODO simulate solves with rattler? https://github.com/anaconda/rbr-tooling/blob/main/scripts/multi-versions-stats.py - # TODO Identify edge cases. (Weird constraints...) - skip_log = False - if "py39" in fn or "py310" in fn or "py311" in fn or "py312" in fn: - if name not in ["anaconda", "_anaconda_depends"]: - for i, dep in enumerate(depends): - if dep.split()[0] in ["numpy", "numpy-base"]: - update_numpy_dependencies(depends, record, "dep") - elif skip_log: - logger.debug(f"numpy 2.0.0 skip {fn}") - for i, constrain in enumerate(constrains): - if constrain.split()[0] in ["numpy", "numpy-base"]: - update_numpy_dependencies(constrains, record, "constr") - break - elif skip_log: - logger.debug(f"numpy 2.0.0 skip {fn}") + if NUMPY_CHANGES is not {}: + apply_numpy_changes(record, subdir, fn) + ########### # pytorch # ########### @@ -896,7 +891,7 @@ def patch_record_in_place(fn, record, subdir): ###################### # scipy dependencies # ###################### - + depends = [dep for dep in depends if dep is not None] # scipy 1.8 and 1.9 introduce breaking API changes impacting these packages if name == "theano": if version in ["1.0.4", "1.0.5"]: @@ -1131,7 +1126,7 @@ def patch_record_in_place(fn, record, subdir): # kealib 1.4.8 changed sonames, add new upper bound to existing packages replace_dep(depends, "kealib >=1.4.7,<1.5.0a0", "kealib >=1.4.7,<1.4.8.0a0") - + depends = [dep for dep in depends if dep is not None] # Other broad replacements for i, dep in enumerate(depends): # glib is compatible up to the major version @@ -1696,6 +1691,8 @@ def do_hotfixes(base_dir): def main(): base_dir = join(dirname(__file__), CHANNEL_NAME) do_hotfixes(base_dir) + if NUMPY_CHANGES != {}: + write_csv() if __name__ == "__main__": diff --git a/numpy2.py b/numpy2.py new file mode 100644 index 0000000..cc3cb9c --- /dev/null +++ b/numpy2.py @@ -0,0 +1,248 @@ +from os.path import dirname, isdir, isfile, join +from typing import List, Dict, Any, Sequence, Optional +from conda.models.version import VersionOrder +import csv +from collections import defaultdict +import requests +from numpy2_config import numpy2_protect_dict +import logging +import json +import os +import re + +proposed_changes = defaultdict(lambda: defaultdict(list)) + +# Global dictionary to store data for CSV output +csv_data = defaultdict(list) + +# Configure the logging +logging.basicConfig(level=logging.DEBUG, + format='%(asctime)s - %(name)s - %(levelname)s - %(message)s', + handlers=[logging.FileHandler('hotfixes.log', mode='w'), + logging.StreamHandler()]) +# Create a logger object +logger = logging.getLogger(__name__) + +CHANNEL_NAME = "main" +CHANNEL_ALIAS = "https://repo.anaconda.com/pkgs" +SUBDIRS = ( + "noarch", + "linux-32", + "linux-64", + "linux-aarch64", + "linux-armv6l", + "linux-armv7l", + "linux-ppc64le", + "linux-s390x", + "osx-64", + "osx-arm64", + "win-32", + "win-64", +) + +def collect_proposed_change(subdirectory, filename, change_type, original_dependency, updated_dependency, reason): + """ + Collects a proposed change to a dependency for later processing. + + Parameters: + - subdirectory: The subdirectory where the file is located. + - filename: The name of the file being modified. + - change_type: The type of change (e.g., 'version update'). + - original_dependency: The original dependency string. + - updated_dependency: The updated dependency string. + - reason: The reason for the change. + """ + proposed_changes[subdirectory][filename].append({ + "type": change_type, + "original": original_dependency, + "updated": updated_dependency, + "reason": reason + }) + +def parse_version(version_str): + """ + Extracts the version number from a version string. + + Parameters: + - version_str: The version string to parse. + + Returns: + The extracted version number or None if not found. + """ + match = re.search(r'(\d+(\.\d+)*)', version_str) + return match.group(1) if match else None + +def has_upper_bound(dependency): + """ + Checks if a dependency string contains an upper bound. + + Parameters: + - dependency: The dependency string to check. + + Returns: + True if an upper bound is found, False otherwise. + """ + return any(part.strip().startswith('<') for part in dependency.split(',')) + +def patch_record_with_fixed_deps(dependency, parts): + """ + Adds an upper bound to a dependency if necessary. + + Parameters: + - dependency: The original dependency string. + - parts: The parts of the dependency string, split by spaces. + + Returns: + The potentially modified dependency string. + """ + version_str = parts[1] + version = parse_version(version_str) + if version: + if version_str.startswith('==') or version_str.startswith('<') or version_str[0].isdigit(): + return dependency + if version_str.startswith('>') or version_str.startswith('>='): + return f"{dependency},<2.0a0" + return f"{dependency} <2.0a0" + return dependency + +def write_csv(): + """ + Writes collected data to CSV files, one per issue type. + """ + for issue_type, data in csv_data.items(): + filename = f"{issue_type}_numpy2_updates.csv" + with open(filename, 'w', newline='') as csvfile: + writer = csv.writer(csvfile) + writer.writerow(['Package', 'Version', 'Build', 'Build Number', 'Original Dependency', 'Updated Dependency', 'Reason']) + writer.writerows(data) + + +def log_and_collect(issue_type, package_info, original_dependency, updated_dependency, reason): + """ + Logs and collects data on dependency modifications for reporting. + + Parameters: + - issue_type: Type of issue prompting modification. + - package_info: Package name, version, build, and build number. + - original_dependency: Original dependency specification. + - updated_dependency: Updated dependency specification. + - reason: Reason for modification. + """ + logger.info(f"numpy 2.0.0: {issue_type} for {package_info}. Original: '{original_dependency}' -> New: '{updated_dependency}' ({reason})") + name, version, build, build_number = package_info.split(' v')[0], package_info.split(' v')[1].split(' (')[0], package_info.split('build: ')[1].split(',')[0], package_info.split('build_number: ')[1][:-1] + csv_data[issue_type].append([name, version, build, build_number, original_dependency, updated_dependency, reason]) + + +def update_numpy_dependencies(dependencies_list, package_record, dependency_type, package_subdir, filename): + """ + Adds upper bounds to numpy dependencies as needed. + + Iterates through dependencies, modifying those without upper bounds and meeting specific criteria. + + Parameters: + - dependencies_list: Dependencies to check and modify. + - package_record: Metadata about the current package. + - dependency_type: Type of dependency ('run', 'build'). + - package_subdir: Package location subdirectory. + - filename: Package filename. + """ + for i, dependency in enumerate(dependencies_list): + parts = dependency.split() + package_name = parts[0] + + # Check for numpy or numpy-base packages and proceed if found + if package_name in ["numpy", "numpy-base"]: + # Construct package info string for logging + package_info = f"{package_record['name']} v{package_record['version']} (build: {package_record['build']}, build_number: {package_record['build_number']})" + + # Proceed if no upper bound exists in the dependency + if not has_upper_bound(dependency): + # Check if package is in the protection dictionary + if package_name in numpy2_protect_dict: + version_str = parts[1] if len(parts) > 1 else None + version = parse_version(version_str) if version_str else None + protected_version = parse_version(numpy2_protect_dict[package_name]) + + # Attempt to add an upper bound if version conditions are met + if version and protected_version: + try: + if VersionOrder(version) <= VersionOrder(protected_version): + new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" + collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Version <= protected_version") + except ValueError: + new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" + collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Version comparison failed") + else: + collect_proposed_change(package_subdir, filename, dependency_type, dependency, dependency, "Missing version or protected_version") + elif numpy2_protect_dict.get('add_bound_to_unspecified', False): + # Handle dependencies without specified bounds + if len(parts) > 1: + new_dependency = patch_record_with_fixed_deps(dependency, parts) + if new_dependency != dependency: + collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Upper bound added") + else: + collect_proposed_change(package_subdir, filename, dependency_type, dependency, dependency, "No unspecified bound") + else: + new_dependency = f"{dependency} <2.0a0" + collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Upper bound added") + else: + collect_proposed_change(package_subdir, filename, dependency_type, dependency, dependency, "Not in protect_dict, no unspecified bound") + else: + # Log if dependency already has an upper bound + collect_proposed_change(package_subdir, filename, dependency_type, dependency, dependency, "Already has upper bound") + + +def main(): + base_dir = join(dirname(__file__), CHANNEL_NAME) + # Step 1. Collect initial repodata for all subdirs. + repodatas = {} + for subdir in SUBDIRS: + repodata_path = join(base_dir, subdir, "repodata_from_packages.json") + if isfile(repodata_path): + with open(repodata_path) as fh: + repodatas[subdir] = json.load(fh) + else: + repodata_url = "/".join( + (CHANNEL_ALIAS, CHANNEL_NAME, subdir, "repodata_from_packages.json") + ) + response = requests.get(repodata_url) + response.raise_for_status() + repodatas[subdir] = response.json() + if not isdir(dirname(repodata_path)): + os.makedirs(dirname(repodata_path)) + with open(repodata_path, "w") as fh: + json.dump( + repodatas[subdir], + fh, + indent=2, + sort_keys=True, + separators=(",", ": "), + ) + for subdir in SUBDIRS: + index = repodatas[subdir]["packages"] + for fn, record in index.items(): + name = record["name"] + depends = record["depends"] + constrains = record.get("constrains", []) + + depends = [dep for dep in depends if dep is not None] + if "py39" in fn or "py310" in fn or "py311" in fn or "py312" in fn: + if name not in ["anaconda", "_anaconda_depends", "__anaconda_core_depends", "_anaconda_core"]: + try: + for dep in depends: + if dep.split()[0] in ["numpy", "numpy-base"]: + update_numpy_dependencies(depends, record, "dep", subdir, fn) + for constrain in constrains: + if constrain.split()[0] in ["numpy", "numpy-base"]: + update_numpy_dependencies(constrains, record, "constr", subdir, fn) + except Exception as e: + logger.error(f"numpy 2.0.0 error {fn}: {e}") + + # Write proposed changes to a JSON file + with open('proposed_numpy_changes.json', 'w') as f: + json.dump(proposed_changes, f, indent=2) + + logger.info(f"Proposed changes have been written to proposed_numpy_changes.json") + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/numpy2_config.py b/numpy2_config.py index 686564b..a3a25ac 100644 --- a/numpy2_config.py +++ b/numpy2_config.py @@ -2,5 +2,7 @@ 'add_bound_to_unspecified': True, 'pandas': '2.2.2', 'scikit-learn': '1.4.2', + 'pyamg': '4.2.3', + 'pyqtgraph': '0.13.1' # Add more packages as needed } \ No newline at end of file diff --git a/test_numpy.py b/test_numpy.py new file mode 100644 index 0000000..0ced1b6 --- /dev/null +++ b/test_numpy.py @@ -0,0 +1,90 @@ +import json +import os +import pytest +import warnings +warnings.filterwarnings("ignore", category=DeprecationWarning, module="boltons.timeutils") +from main import SUBDIRS # Import SUBDIRS from your main script + + + +@pytest.fixture +def json_data(): + """Fixture to load the JSON data from the output file.""" + json_file = 'proposed_numpy_changes.json' + if not os.path.exists(json_file): + pytest.skip(f"{json_file} not found. Run the main script first.") + with open(json_file, 'r') as f: + return json.load(f) + +def test_json_structure(json_data): + """Test the overall structure of the JSON output.""" + assert isinstance(json_data, dict), "JSON root should be a dictionary" + + # Check if at least one subdir is present + assert any(subdir in json_data for subdir in SUBDIRS), "At least one subdir should be in the JSON output" + + for subdir in json_data: + assert subdir in SUBDIRS, f"Unexpected subdir {subdir} in the JSON output" + assert isinstance(json_data[subdir], dict), f"Subdir {subdir} should contain a dictionary" + + # Log which subdirs are missing + missing_subdirs = [subdir for subdir in SUBDIRS if subdir not in json_data] + if missing_subdirs: + print(f"Note: The following subdirs are not present in the JSON output: {', '.join(missing_subdirs)}") + +def test_package_structure(json_data): + """Test the structure of each package entry.""" + for subdir, packages in json_data.items(): + for package, changes in packages.items(): + assert isinstance(changes, list), f"Changes for {package} in {subdir} should be a list" + for change in changes: + assert isinstance(change, dict), f"Each change for {package} in {subdir} should be a dictionary" + assert set(change.keys()) == {'type', 'original', 'updated', 'reason'}, \ + f"Change for {package} in {subdir} has incorrect keys" + +def test_change_types(json_data): + """Test that change types are either 'dep' or 'constr'.""" + valid_types = {'dep', 'constr'} + for subdir, packages in json_data.items(): + for package, changes in packages.items(): + for change in changes: + assert change['type'] in valid_types, \ + f"Invalid change type for {package} in {subdir}: {change['type']}" + +def test_numpy_changes(json_data): + """Test that changes are related to numpy or numpy-base.""" + for subdir, packages in json_data.items(): + for package, changes in packages.items(): + for change in changes: + assert 'numpy' in change['original'].lower() or 'numpy-base' in change['original'].lower(), \ + f"Change for {package} in {subdir} is not related to numpy: {change['original']}" + +def test_version_bounds(json_data): + """Test that updated dependencies have the correct version bounds.""" + for subdir, packages in json_data.items(): + for package, changes in packages.items(): + for change in changes: + if change['original'] != change['updated']: + assert '<2.0a0' in change['updated'], \ + f"Updated dependency for {package} in {subdir} doesn't have correct upper bound: {change['updated']}" + +def test_reason_provided(json_data): + """Test that each change has a non-empty reason.""" + for subdir, packages in json_data.items(): + for package, changes in packages.items(): + for change in changes: + assert change['reason'], f"Change for {package} in {subdir} has no reason provided" + +def test_no_empty_changes(json_data): + """Test that there are no packages with empty change lists.""" + for subdir, packages in json_data.items(): + for package, changes in packages.items(): + assert changes, f"Package {package} in {subdir} has no changes" + +def test_changes_present(json_data): + """Test that there are actually changes in the output.""" + assert json_data, "JSON output should not be empty" + assert any(packages for packages in json_data.values()), "At least one subdir should have changes" + +if __name__ == '__main__': + pytest.main([__file__]) \ No newline at end of file From 18e3c4d9b08d344f0c3b6c41f826c8c88e5104bd Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 25 Jul 2024 10:13:05 +0100 Subject: [PATCH 18/47] formatting changes --- main.py | 2 +- numpy2.py | 1 - test-hotfix.py | 3 ++- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/main.py b/main.py index f3656dd..a551945 100644 --- a/main.py +++ b/main.py @@ -9,7 +9,7 @@ from collections import defaultdict from os.path import dirname, isdir, isfile, join import rattler -from typing import List, Dict, Any, Sequence, Optional +from typing import List, Sequence from conda.models.version import VersionOrder import csv from collections import defaultdict diff --git a/numpy2.py b/numpy2.py index cc3cb9c..e6f0135 100644 --- a/numpy2.py +++ b/numpy2.py @@ -1,5 +1,4 @@ from os.path import dirname, isdir, isfile, join -from typing import List, Dict, Any, Sequence, Optional from conda.models.version import VersionOrder import csv from collections import defaultdict diff --git a/test-hotfix.py b/test-hotfix.py index 2fa7581..5b668e2 100644 --- a/test-hotfix.py +++ b/test-hotfix.py @@ -18,7 +18,8 @@ channel_map = { "main": "https://repo.anaconda.com/pkgs/main", "r": "https://repo.anaconda.com/pkgs/r", - "msys2": "https://repo.anaconda.com/pkgs/msys2" + "msys2": "https://repo.anaconda.com/pkgs/msys2", + "numpy2": "https://anaconda.org/ad-testing/numpy", } From e3cb04bd8554710c2b26dceed01a15528186886a Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 25 Jul 2024 10:21:18 +0100 Subject: [PATCH 19/47] main trimmed whitespace --- main.py | 28 +++++++++++++--------------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/main.py b/main.py index a551945..6d5f09d 100644 --- a/main.py +++ b/main.py @@ -12,10 +12,7 @@ from typing import List, Sequence from conda.models.version import VersionOrder import csv -from collections import defaultdict import requests -from numpy2_config import numpy2_protect_dict - import logging # Global dictionary to store data for CSV output @@ -284,9 +281,8 @@ def load_numpy_changes(): except FileNotFoundError: logger.warning("proposed_numpy_changes.json not found. No numpy changes will be applied.") return {} - + NUMPY_CHANGES = load_numpy_changes() - def apply_numpy_changes(record, subdir, filename): """ @@ -308,6 +304,7 @@ def apply_numpy_changes(record, subdir, filename): _apply_changes_to_dependencies(depends, change, record, filename, 'type') + def _get_dependency_list(record, change_type): """ Returns the appropriate dependency list based on the change type. @@ -325,6 +322,7 @@ def _get_dependency_list(record, change_type): return record.get('constrains', []) return None + def _apply_changes_to_dependencies(depends, change, record, filename, sort_type='reason'): """ Applies changes to dependencies and logs the changes. @@ -343,8 +341,8 @@ def _apply_changes_to_dependencies(depends, change, record, filename, sort_type= logger.info(f"Applied numpy change for {filename}: {change['original']} -> {change['updated']}") # Add to csv_data for later CSV export csv_data[change[sort_type]].append([ - record['name'], record['version'], record['build'], - record['build_number'], change['original'], + record['name'], record['version'], record['build'], + record['build_number'], change['original'], change['updated'], change['reason'] ]) @@ -365,13 +363,13 @@ async def solve_dependencies( version = record.version._source build = record.build package_spec = rattler.MatchSpec(f"{name}={version}={build}") - + # Create MatchSpecs for all dependencies dep_specs = [rattler.MatchSpec(dep) for dep in record.depends] - + # Combine the package spec and dependency specs all_specs = [package_spec] + dep_specs - + # Solve dependencies solved_packages = await rattler.solve( channels=channels, @@ -394,7 +392,7 @@ def write_csv(): """ if not os.path.exists("updates"): os.makedirs("updates") - + for issue_type, data in csv_data.items(): with open(f"updates/{issue_type}_numpy2_updates.csv", 'w', newline='') as csvfile: csv.writer(csvfile).writerow(['Package', 'Version', 'Build', 'Build Number', 'Original Dependency', 'Updated Dependency', 'Reason']) @@ -600,16 +598,16 @@ def _fix_cudnn_depends(depends, subdir): depends[idx] = correct_cudnn_depends def filter_packages(repo_data, substring): - + # Initialize the new dictionary to store filtered results filtered_dict = {} - + # Loop through each key-value pair in the 'Packages' dictionary for key, value in repo_data.items(): # If the key contains the desired substring, add it to the filtered dictionary if substring in key: filtered_dict[key] = value - + return filtered_dict def _patch_repodata(repodata, subdir): @@ -827,7 +825,7 @@ def patch_record_in_place(fn, record, subdir): if NUMPY_CHANGES is not {}: apply_numpy_changes(record, subdir, fn) - + ########### # pytorch # ########### From 86c54a15c6866383b644414915486815f993e875 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 25 Jul 2024 10:25:37 +0100 Subject: [PATCH 20/47] repair lint issues --- main.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/main.py b/main.py index 6d5f09d..dc1b5bb 100644 --- a/main.py +++ b/main.py @@ -282,8 +282,10 @@ def load_numpy_changes(): logger.warning("proposed_numpy_changes.json not found. No numpy changes will be applied.") return {} + NUMPY_CHANGES = load_numpy_changes() + def apply_numpy_changes(record, subdir, filename): """ Applies predefined numpy changes to a record based on its directory and filename. @@ -295,13 +297,11 @@ def apply_numpy_changes(record, subdir, filename): """ if subdir not in NUMPY_CHANGES or filename not in NUMPY_CHANGES[subdir]: return - changes = NUMPY_CHANGES[subdir][filename] for change in changes: depends = _get_dependency_list(record, change['type']) if depends is None: continue - _apply_changes_to_dependencies(depends, change, record, filename, 'type') @@ -329,7 +329,7 @@ def _apply_changes_to_dependencies(depends, change, record, filename, sort_type= Parameters: - depends (list): The list of dependencies to be modified. - - change (dict): A dictionary containing the 'original' dependency, the 'updated' dependency, and the 'reason' for the change. + - change (dict): A dictionary containing the 'original' dependency, the 'updated' dependency, the 'reason' for the change. - record (dict): The record to which the changes apply. - filename (str): The name of the file being processed. - sort_type (str, optional): The key in the 'change' dictionary to sort the CSV data by. Defaults to 'reason'. @@ -395,7 +395,10 @@ def write_csv(): for issue_type, data in csv_data.items(): with open(f"updates/{issue_type}_numpy2_updates.csv", 'w', newline='') as csvfile: - csv.writer(csvfile).writerow(['Package', 'Version', 'Build', 'Build Number', 'Original Dependency', 'Updated Dependency', 'Reason']) + csv.writer(csvfile).writerow(['Package', 'Version', + 'Build', 'Build Number', + 'Original Dependency', 'Updated Dependency', + 'Reason']) csv.writer(csvfile).writerows(data) @@ -597,6 +600,7 @@ def _fix_cudnn_depends(depends, subdir): idx = depends.index(original_cudnn_depend) depends[idx] = correct_cudnn_depends + def filter_packages(repo_data, substring): # Initialize the new dictionary to store filtered results @@ -610,6 +614,7 @@ def filter_packages(repo_data, substring): return filtered_dict + def _patch_repodata(repodata, subdir): index = repodata["packages"] instructions = { From 0027dab2a324fdf6bf3c3cad54616e01746f6e90 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 25 Jul 2024 10:42:08 +0100 Subject: [PATCH 21/47] remove all the lint errors from flake --- main.py | 11 ++++--- numpy2.py | 86 ++++++++++++++++++++++++++---------------------- numpy2_config.py | 2 +- test_numpy.py | 27 ++++++++++----- 4 files changed, 72 insertions(+), 54 deletions(-) diff --git a/main.py b/main.py index dc1b5bb..6a6be56 100644 --- a/main.py +++ b/main.py @@ -274,6 +274,7 @@ "_anaconda_depends", ] + def load_numpy_changes(): try: with open('proposed_numpy_changes.json', 'r') as f: @@ -314,7 +315,7 @@ def _get_dependency_list(record, change_type): - change_type (str): The type of change ('dep' for dependencies, 'constr' for constraints). Returns: - - list: The list of dependencies or constraints based on the change type, or None if the change type is unrecognized. + - list: The list of dependencies or constraints based on the change type, None if the change type is unrecognized. """ if change_type == 'dep': return record['depends'] @@ -329,7 +330,7 @@ def _apply_changes_to_dependencies(depends, change, record, filename, sort_type= Parameters: - depends (list): The list of dependencies to be modified. - - change (dict): A dictionary containing the 'original' dependency, the 'updated' dependency, the 'reason' for the change. + - change (dict): A dict containing the original dependency, the updated dependency, the reason for the change. - record (dict): The record to which the changes apply. - filename (str): The name of the file being processed. - sort_type (str, optional): The key in the 'change' dictionary to sort the CSV data by. Defaults to 'reason'. @@ -395,9 +396,9 @@ def write_csv(): for issue_type, data in csv_data.items(): with open(f"updates/{issue_type}_numpy2_updates.csv", 'w', newline='') as csvfile: - csv.writer(csvfile).writerow(['Package', 'Version', - 'Build', 'Build Number', - 'Original Dependency', 'Updated Dependency', + csv.writer(csvfile).writerow(['Package', 'Version', + 'Build', 'Build Number', + 'Original Dependency', 'Updated Dependency', 'Reason']) csv.writer(csvfile).writerows(data) diff --git a/numpy2.py b/numpy2.py index e6f0135..3a85348 100644 --- a/numpy2.py +++ b/numpy2.py @@ -39,10 +39,11 @@ "win-64", ) + def collect_proposed_change(subdirectory, filename, change_type, original_dependency, updated_dependency, reason): """ Collects a proposed change to a dependency for later processing. - + Parameters: - subdirectory: The subdirectory where the file is located. - filename: The name of the file being modified. @@ -58,39 +59,42 @@ def collect_proposed_change(subdirectory, filename, change_type, original_depend "reason": reason }) + def parse_version(version_str): """ Extracts the version number from a version string. - + Parameters: - version_str: The version string to parse. - + Returns: The extracted version number or None if not found. """ match = re.search(r'(\d+(\.\d+)*)', version_str) return match.group(1) if match else None + def has_upper_bound(dependency): """ Checks if a dependency string contains an upper bound. - + Parameters: - dependency: The dependency string to check. - + Returns: True if an upper bound is found, False otherwise. """ return any(part.strip().startswith('<') for part in dependency.split(',')) + def patch_record_with_fixed_deps(dependency, parts): """ Adds an upper bound to a dependency if necessary. - + Parameters: - dependency: The original dependency string. - parts: The parts of the dependency string, split by spaces. - + Returns: The potentially modified dependency string. """ @@ -104,6 +108,7 @@ def patch_record_with_fixed_deps(dependency, parts): return f"{dependency} <2.0a0" return dependency + def write_csv(): """ Writes collected data to CSV files, one per issue type. @@ -112,14 +117,15 @@ def write_csv(): filename = f"{issue_type}_numpy2_updates.csv" with open(filename, 'w', newline='') as csvfile: writer = csv.writer(csvfile) - writer.writerow(['Package', 'Version', 'Build', 'Build Number', 'Original Dependency', 'Updated Dependency', 'Reason']) + writer.writerow(['Package', 'Version', 'Build', 'Build Number', + 'Original Dependency', 'Updated Dependency', 'Reason']) writer.writerows(data) def log_and_collect(issue_type, package_info, original_dependency, updated_dependency, reason): """ Logs and collects data on dependency modifications for reporting. - + Parameters: - issue_type: Type of issue prompting modification. - package_info: Package name, version, build, and build number. @@ -127,17 +133,20 @@ def log_and_collect(issue_type, package_info, original_dependency, updated_depen - updated_dependency: Updated dependency specification. - reason: Reason for modification. """ - logger.info(f"numpy 2.0.0: {issue_type} for {package_info}. Original: '{original_dependency}' -> New: '{updated_dependency}' ({reason})") - name, version, build, build_number = package_info.split(' v')[0], package_info.split(' v')[1].split(' (')[0], package_info.split('build: ')[1].split(',')[0], package_info.split('build_number: ')[1][:-1] + logger.info(f"numpy 2.0.0: {issue_type} for {package_info}. " + f"Original: '{original_dependency}' -> New: '{updated_dependency}' ({reason})") + + name, version = package_info.split(' v')[0], package_info.split(' v')[1].split(' (')[0] + build = package_info.split('build: ')[1].split(',')[0] + build_number = package_info.split('build_number: ')[1][:-1] csv_data[issue_type].append([name, version, build, build_number, original_dependency, updated_dependency, reason]) def update_numpy_dependencies(dependencies_list, package_record, dependency_type, package_subdir, filename): """ Adds upper bounds to numpy dependencies as needed. - Iterates through dependencies, modifying those without upper bounds and meeting specific criteria. - + Parameters: - dependencies_list: Dependencies to check and modify. - package_record: Metadata about the current package. @@ -148,47 +157,44 @@ def update_numpy_dependencies(dependencies_list, package_record, dependency_type for i, dependency in enumerate(dependencies_list): parts = dependency.split() package_name = parts[0] - - # Check for numpy or numpy-base packages and proceed if found if package_name in ["numpy", "numpy-base"]: - # Construct package info string for logging - package_info = f"{package_record['name']} v{package_record['version']} (build: {package_record['build']}, build_number: {package_record['build_number']})" - - # Proceed if no upper bound exists in the dependency if not has_upper_bound(dependency): - # Check if package is in the protection dictionary if package_name in numpy2_protect_dict: version_str = parts[1] if len(parts) > 1 else None version = parse_version(version_str) if version_str else None protected_version = parse_version(numpy2_protect_dict[package_name]) - - # Attempt to add an upper bound if version conditions are met if version and protected_version: try: if VersionOrder(version) <= VersionOrder(protected_version): new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" - collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Version <= protected_version") + collect_proposed_change(package_subdir, filename, dependency_type, dependency, + new_dependency, "Version <= protected_version") except ValueError: new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" - collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Version comparison failed") + collect_proposed_change(package_subdir, filename, dependency_type, dependency, + new_dependency, "Version comparison failed") else: - collect_proposed_change(package_subdir, filename, dependency_type, dependency, dependency, "Missing version or protected_version") + collect_proposed_change(package_subdir, filename, dependency_type, dependency, + dependency, "Missing version or protected_version") elif numpy2_protect_dict.get('add_bound_to_unspecified', False): - # Handle dependencies without specified bounds if len(parts) > 1: new_dependency = patch_record_with_fixed_deps(dependency, parts) if new_dependency != dependency: - collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Upper bound added") + collect_proposed_change(package_subdir, filename, dependency_type, dependency, + new_dependency, "Upper bound added") else: - collect_proposed_change(package_subdir, filename, dependency_type, dependency, dependency, "No unspecified bound") + collect_proposed_change(package_subdir, filename, dependency_type, dependency, + dependency, "No unspecified bound") else: new_dependency = f"{dependency} <2.0a0" - collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Upper bound added") + collect_proposed_change(package_subdir, filename, dependency_type, dependency, + new_dependency, "Upper bound added") else: - collect_proposed_change(package_subdir, filename, dependency_type, dependency, dependency, "Not in protect_dict, no unspecified bound") + collect_proposed_change(package_subdir, filename, dependency_type, dependency, + dependency, "Not in protect_dict, no unspecified bound") else: - # Log if dependency already has an upper bound - collect_proposed_change(package_subdir, filename, dependency_type, dependency, dependency, "Already has upper bound") + collect_proposed_change(package_subdir, filename, dependency_type, dependency, + dependency, "Already has upper bound") def main(): @@ -225,9 +231,9 @@ def main(): constrains = record.get("constrains", []) depends = [dep for dep in depends if dep is not None] - if "py39" in fn or "py310" in fn or "py311" in fn or "py312" in fn: + if "py39" in fn or "py310" in fn or "py311" in fn or "py312" in fn: if name not in ["anaconda", "_anaconda_depends", "__anaconda_core_depends", "_anaconda_core"]: - try: + try: for dep in depends: if dep.split()[0] in ["numpy", "numpy-base"]: update_numpy_dependencies(depends, record, "dep", subdir, fn) @@ -236,12 +242,14 @@ def main(): update_numpy_dependencies(constrains, record, "constr", subdir, fn) except Exception as e: logger.error(f"numpy 2.0.0 error {fn}: {e}") - + # Write proposed changes to a JSON file - with open('proposed_numpy_changes.json', 'w') as f: + json_filename = "proposed_numpy_changes.json" + with open(json_filename, 'w') as f: json.dump(proposed_changes, f, indent=2) - logger.info(f"Proposed changes have been written to proposed_numpy_changes.json") - + logger.info(f"Proposed changes have been written to {json_filename}") + + if __name__ == "__main__": - main() \ No newline at end of file + main() diff --git a/numpy2_config.py b/numpy2_config.py index a3a25ac..be1389e 100644 --- a/numpy2_config.py +++ b/numpy2_config.py @@ -5,4 +5,4 @@ 'pyamg': '4.2.3', 'pyqtgraph': '0.13.1' # Add more packages as needed -} \ No newline at end of file +} diff --git a/test_numpy.py b/test_numpy.py index 0ced1b6..bf248f9 100644 --- a/test_numpy.py +++ b/test_numpy.py @@ -1,10 +1,8 @@ +from main import SUBDIRS # Import SUBDIRS from your main script + import json import os import pytest -import warnings -warnings.filterwarnings("ignore", category=DeprecationWarning, module="boltons.timeutils") -from main import SUBDIRS # Import SUBDIRS from your main script - @pytest.fixture @@ -16,13 +14,14 @@ def json_data(): with open(json_file, 'r') as f: return json.load(f) + def test_json_structure(json_data): """Test the overall structure of the JSON output.""" assert isinstance(json_data, dict), "JSON root should be a dictionary" - + # Check if at least one subdir is present assert any(subdir in json_data for subdir in SUBDIRS), "At least one subdir should be in the JSON output" - + for subdir in json_data: assert subdir in SUBDIRS, f"Unexpected subdir {subdir} in the JSON output" assert isinstance(json_data[subdir], dict), f"Subdir {subdir} should contain a dictionary" @@ -32,6 +31,7 @@ def test_json_structure(json_data): if missing_subdirs: print(f"Note: The following subdirs are not present in the JSON output: {', '.join(missing_subdirs)}") + def test_package_structure(json_data): """Test the structure of each package entry.""" for subdir, packages in json_data.items(): @@ -42,6 +42,7 @@ def test_package_structure(json_data): assert set(change.keys()) == {'type', 'original', 'updated', 'reason'}, \ f"Change for {package} in {subdir} has incorrect keys" + def test_change_types(json_data): """Test that change types are either 'dep' or 'constr'.""" valid_types = {'dep', 'constr'} @@ -51,6 +52,7 @@ def test_change_types(json_data): assert change['type'] in valid_types, \ f"Invalid change type for {package} in {subdir}: {change['type']}" + def test_numpy_changes(json_data): """Test that changes are related to numpy or numpy-base.""" for subdir, packages in json_data.items(): @@ -59,14 +61,18 @@ def test_numpy_changes(json_data): assert 'numpy' in change['original'].lower() or 'numpy-base' in change['original'].lower(), \ f"Change for {package} in {subdir} is not related to numpy: {change['original']}" + def test_version_bounds(json_data): """Test that updated dependencies have the correct version bounds.""" for subdir, packages in json_data.items(): for package, changes in packages.items(): for change in changes: if change['original'] != change['updated']: - assert '<2.0a0' in change['updated'], \ - f"Updated dependency for {package} in {subdir} doesn't have correct upper bound: {change['updated']}" + assert '<2.0a0' in change['updated'], ( + f"Updated dependency for {package} in {subdir} " + f"doesn't have correct upper bound: {change['updated']}" + ) + def test_reason_provided(json_data): """Test that each change has a non-empty reason.""" @@ -75,16 +81,19 @@ def test_reason_provided(json_data): for change in changes: assert change['reason'], f"Change for {package} in {subdir} has no reason provided" + def test_no_empty_changes(json_data): """Test that there are no packages with empty change lists.""" for subdir, packages in json_data.items(): for package, changes in packages.items(): assert changes, f"Package {package} in {subdir} has no changes" + def test_changes_present(json_data): """Test that there are actually changes in the output.""" assert json_data, "JSON output should not be empty" assert any(packages for packages in json_data.values()), "At least one subdir should have changes" + if __name__ == '__main__': - pytest.main([__file__]) \ No newline at end of file + pytest.main([__file__]) From 571832bcd7b9c4fda443bee48c3c4be031f820ab Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 25 Jul 2024 10:46:31 +0100 Subject: [PATCH 22/47] revert test-hotfix --- test-hotfix.py | 1 - 1 file changed, 1 deletion(-) diff --git a/test-hotfix.py b/test-hotfix.py index 5b668e2..b2d40eb 100644 --- a/test-hotfix.py +++ b/test-hotfix.py @@ -19,7 +19,6 @@ "main": "https://repo.anaconda.com/pkgs/main", "r": "https://repo.anaconda.com/pkgs/r", "msys2": "https://repo.anaconda.com/pkgs/msys2", - "numpy2": "https://anaconda.org/ad-testing/numpy", } From 34f2d32696f9cf6370e5b6149d97645f5148cb9c Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 25 Jul 2024 10:49:32 +0100 Subject: [PATCH 23/47] py-rattler adding --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e56670d..f061e17 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,7 +19,7 @@ jobs: - name: Setup environment shell: bash -l {0} run: | - conda create --name testenv conda conda-index flake8 requests + conda create --name testenv conda conda-index flake8 requests conda-forge::py-rattler - name: Lint shell: bash -l {0} run: | From fec2680e4a9fc90d332cf0f9723ae46500b7e0fc Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 25 Jul 2024 14:55:12 +0100 Subject: [PATCH 24/47] add to readme the new processes --- README.md | 89 +++++++++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 76 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 28fe6cc..0adc229 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # repodata-hotfixes ## Changes to package metadata to fix behavior -When packages are created, authors do their best to specify constraints that make their package work. Sometimes things change, and their constraints are not accurate for making things work. This results in broken environments. People need to be able to patch the package metadata long after the packages are built, so that we can prevent conda from creating broken environments. This repository holds python scripts that generate JSON files, which are then applied on top of the repodata.json index files that are generated from the original package content. +When packages are created, authors do their best to specify constraints that make their package work. Sometimes things change, and their constraints are not accurate for making things work. This results in broken environments. People need to be able to patch the package metadata long after the packages are built, so that we can prevent conda from creating broken environments. This repository holds python scripts that generate JSON files, which are then applied on top of the repodata.json index files that are generated from the original package content. ## Things that may require a metadata hotfix: @@ -13,25 +13,25 @@ When packages are created, authors do their best to specify constraints that mak ### Dependency and Constraint updates -Changing dependencies and constraints is the primary reason hotfixes are applied. Their +Changing dependencies and constraints is the primary reason hotfixes are applied. Their may be reasons why you need to change a longstanding package but rebuilding may not be -feasible or perhaps not worth the time. By changing dependencies and constraints, +feasible or perhaps not worth the time. By changing dependencies and constraints, the data used to solve for dependencies can be modified and leave the larger ecosystem unharmed. -NOTE: Hotfixes are applied in a overwrite manner. So any changes are implemented +NOTE: Hotfixes are applied in a overwrite manner. So any changes are implemented will effect the the entire dependency or constraint list (i.e. If someone changes one out of the ten dependency for a single package, all ten will still should be in the "patch-instructions" as patching is an overwriting operation). ### Removal -Adding a package to the removal list will remove the entire entry from the repodata.json. It will no longer be searchable by conda search. +Adding a package to the removal list will remove the entire entry from the repodata.json. It will no longer be searchable by conda search. We should put things on the remove list when: - We need a quick fix to stop consumers from downloading a bad package. -Another approach might be to move the package into broken package directory (see directions in perseverance-skills). This will cause it not to be indexed in the first place. +Another approach might be to move the package into broken package directory (see directions in perseverance-skills). This will cause it not to be indexed in the first place. ### Revoked @@ -45,12 +45,76 @@ We should put things on the revoke list when: - We feel we want a customer to still have access but not the whole consumer population by default - ? +## Numpy 2.0 Compatibility Checks and Updates + +### Running numpy2.py + +The `numpy2.py` script is used to check and update package dependencies for compatibility with numpy 2.0. To run the script, use the following command: + +``` +python numpy2.py +``` + +### What numpy2.py does + +`numpy2.py` performs the following tasks: +1. Scans through the repodata for packages depending on numpy. +2. Checks if these dependencies need updates to ensure compatibility with numpy 2.0. +3. Proposes changes to add upper bounds to numpy dependencies where necessary. +4. Generates a `proposed_numpy_changes.json` file containing all proposed changes. + +### When to use numpy2.py + +Use `numpy2.py` when: +- Preparing for a major numpy version update (e.g., transitioning to numpy 2.0). +- You need to audit and update numpy dependencies across many packages. +- You want to ensure compatibility of the ecosystem with upcoming numpy versions. + +### Running main.py with proposed_numpy_changes.json + +After running `numpy2.py`, you'll have a `proposed_numpy_changes.json` file. To apply these changes: + +1. Ensure `proposed_numpy_changes.json` is in the same directory as `main.py`. +2. Run `main.py` as usual: + +``` +python main.py +``` + +`main.py` will automatically detect and incorporate the changes from `proposed_numpy_changes.json` into the hotfix process. + +## Reviewing CSV Updates + +After running `numpy2.py` or `main.py`, CSV files are generated containing detailed information about the proposed changes. To review these updates: + +1. Locate the generated CSV files in your working directory. They will be named according to the type of update, e.g., `dep_numpy2_updates.csv`, `constr_numpy2_updates.csv`. + +2. For a quick review, you can open these files with any spreadsheet application on your local machine. + +3. For a more collaborative review or to share the updates with your team, you can upload the CSV files to a cloud-based service: + + - Google Sheets: + 1. Go to [Google Sheets](https://sheets.google.com). + 2. Click on "Blank" to create a new spreadsheet. + 3. Go to File > Import > Upload and select your CSV file. + 4. Choose your import options and click "Import data". + +4. Once uploaded, you can easily sort, filter, and analyze the proposed changes. Look for: + - Packages affected + - Types of changes (e.g., adding upper bounds, modifying existing bounds) + - Reasons for changes + +5. Use this review to make informed decisions about which changes to approve or modify before applying the hotfixes. + +Remember to handle these CSVs securely, especially if they contain sensitive package information. + ## Utility scripts: + ### Seeing current hotfixes with `gen-current-hotfix-report.py`: -It can be quite difficult to grok what the hotfix scripts are doing. The script, `gen-current-hotfix-report.py`, attempts to make it easier to see what the current state of the applied hotfixes looks like. +It can be quite difficult to grok what the hotfix scripts are doing. The script, `gen-current-hotfix-report.py`, attempts to make it easier to see what the current state of the applied hotfixes looks like. -The script downloads the current repodata. It then shows you a diff. Example usage of this script: +The script downloads the current repodata. It then shows you a diff. Example usage of this script: ``` python gen-current-hotfix-report.py main --subdir linux-64 osx-64 win-64 osx-arm64 linux-ppc64le linux-aarch64 linux-s390x noarch @@ -60,16 +124,15 @@ For repeated runs add `--use-cache` to avoid downloading the repodata files. ### Testing hotfixes with `test-hotfix.py`: -The script, `test-hotfix.py`, downloads the current repodata and runs your instructions against it. It then shows you a diff. - -This useful for testing out changes before they are committed and deployed. This will show differences in current state of hotfixes +The script, `test-hotfix.py`, downloads the current repodata and runs your instructions against it. It then shows you a diff. +This useful for testing out changes before they are committed and deployed. This will show differences in current state of hotfixes and the ones you are working on. Example usage of this script: + ``` python test-hotfix.py main --subdir linux-64 osx-64 win-64 osx-arm64 linux-ppc64le linux-aarch64 linux-s390x noarch ``` Use the `--color` or `--show-pkgs` options for different outputs. - -For repeated runs add `--use-cache` to avoid downloading the repodata files. +For repeated runs add `--use-cache` to avoid downloading the repodata files. \ No newline at end of file From ed2659a908ac61875012cd677d6f1eb0ea1f084a Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 25 Jul 2024 14:58:26 +0100 Subject: [PATCH 25/47] remove dep none remover --- main.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/main.py b/main.py index 6a6be56..d13b7ef 100644 --- a/main.py +++ b/main.py @@ -704,8 +704,6 @@ def patch_record_in_place(fn, record, subdir): depends = record["depends"] constrains = record.get("constrains", []) - # depends = [dep for dep in depends if dep is not None] - ########## # subdir # ########## @@ -895,7 +893,6 @@ def patch_record_in_place(fn, record, subdir): ###################### # scipy dependencies # ###################### - depends = [dep for dep in depends if dep is not None] # scipy 1.8 and 1.9 introduce breaking API changes impacting these packages if name == "theano": if version in ["1.0.4", "1.0.5"]: @@ -1130,7 +1127,6 @@ def patch_record_in_place(fn, record, subdir): # kealib 1.4.8 changed sonames, add new upper bound to existing packages replace_dep(depends, "kealib >=1.4.7,<1.5.0a0", "kealib >=1.4.7,<1.4.8.0a0") - depends = [dep for dep in depends if dep is not None] # Other broad replacements for i, dep in enumerate(depends): # glib is compatible up to the major version From 4d654e51bda43d93110d1e17f2ecc277710ec460 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 25 Jul 2024 15:17:41 +0100 Subject: [PATCH 26/47] remove yaml --- numpy2_protect.yaml | 6 ------ 1 file changed, 6 deletions(-) delete mode 100644 numpy2_protect.yaml diff --git a/numpy2_protect.yaml b/numpy2_protect.yaml deleted file mode 100644 index 719fb85..0000000 --- a/numpy2_protect.yaml +++ /dev/null @@ -1,6 +0,0 @@ -add_bound_to_unspecified: true # Set to true if you want to add bounds to unlisted packages -numpy: '1.25.0' -numpy-base: '1.25.0' -pandas: '2.2.2' -scikit-learn: '1.4.2' -# Add more packages as needed \ No newline at end of file From c26a1fdcd09b5da6e86c632cffe242e10516c041 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 25 Jul 2024 17:26:02 +0100 Subject: [PATCH 27/47] upload proposed changes --- proposed_numpy_changes.json | 114308 +++++++++++++++++++++++++++++++++ 1 file changed, 114308 insertions(+) create mode 100644 proposed_numpy_changes.json diff --git a/proposed_numpy_changes.json b/proposed_numpy_changes.json new file mode 100644 index 0000000..a96afcf --- /dev/null +++ b/proposed_numpy_changes.json @@ -0,0 +1,114308 @@ +{ + "linux-64": { + "adtk-0.6.2-py310h2f386ee_0.tar.bz2": [ + { + "type": "dep", + "original": "numpy >=1.21.5,<2.0a0", + "updated": "numpy >=1.21.5,<2.0a0", + "reason": "Already has upper bound" + } + ], + "adtk-0.6.2-py310h2f386ee_1.tar.bz2": [ + { + "type": "dep", + "original": "numpy >=1.21.5,<2.0a0", + "updated": "numpy >=1.21.5,<2.0a0", + "reason": "Already has upper bound" + } + ], + "adtk-0.6.2-py311h92b7b1e_1.tar.bz2": [ + { + "type": "dep", + "original": "numpy >=1.23.5,<2.0a0", + "updated": "numpy >=1.23.5,<2.0a0", + "reason": "Already has upper bound" + } + ], + "adtk-0.6.2-py312he106c6f_1.tar.bz2": [ + { + "type": "dep", + "original": "numpy >=1.26.2,<2.0a0", + "updated": "numpy >=1.26.2,<2.0a0", + "reason": "Already has upper bound" + } + ], + "adtk-0.6.2-py39hb070fc8_0.tar.bz2": [ + { + "type": "dep", + "original": "numpy >=1.16.6,<2.0a0", + "updated": "numpy >=1.16.6,<2.0a0", + "reason": "Already has upper bound" + } + ], + "adtk-0.6.2-py39hb070fc8_1.tar.bz2": [ + { + "type": "dep", + "original": "numpy >=1.16.6,<2.0a0", + "updated": "numpy >=1.16.6,<2.0a0", + "reason": "Already has upper bound" + } + ], + "altair-4.2.2-py310h06a4308_0.tar.bz2": [ + { + "type": "dep", + "original": "numpy", + "updated": "numpy <2.0a0", + "reason": "Upper bound added" + } + ], + "altair-4.2.2-py311h06a4308_0.tar.bz2": [ + { + "type": "dep", + "original": "numpy", + "updated": "numpy <2.0a0", + "reason": "Upper bound added" + } + ], + "altair-4.2.2-py39h06a4308_0.tar.bz2": [ + { + "type": "dep", + "original": "numpy", + "updated": "numpy <2.0a0", + "reason": "Upper bound added" + } + ], + "altair-5.0.1-py310h06a4308_0.tar.bz2": [ + { + "type": "dep", + "original": "numpy", + "updated": "numpy <2.0a0", + "reason": "Upper bound added" + } + ], + "altair-5.0.1-py311h06a4308_0.tar.bz2": [ + { + "type": "dep", + "original": "numpy", + "updated": "numpy <2.0a0", + "reason": "Upper bound added" + } + ], + "altair-5.0.1-py312h06a4308_0.tar.bz2": [ + { + "type": "dep", + "original": "numpy", + "updated": "numpy <2.0a0", + "reason": "Upper bound added" + } + ], + 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"dep", + "original": "numpy >=1.16.6,<2.0a0", + "updated": "numpy >=1.16.6,<2.0a0", + "reason": "Already has upper bound" + } + ] + } +} \ No newline at end of file From 71e30cd8fb1547c586ebd31e49e3ae5633d880a4 Mon Sep 17 00:00:00 2001 From: James Robertson Date: Fri, 26 Jul 2024 10:28:10 +0100 Subject: [PATCH 28/47] Apply suggestions from code review Co-authored-by: Charles Bousseau <16641587+cbouss@users.noreply.github.com> --- main.py | 14 -------------- numpy2.py | 5 ----- 2 files changed, 19 deletions(-) diff --git a/main.py b/main.py index d13b7ef..810ffe8 100644 --- a/main.py +++ b/main.py @@ -602,20 +602,6 @@ def _fix_cudnn_depends(depends, subdir): depends[idx] = correct_cudnn_depends -def filter_packages(repo_data, substring): - - # Initialize the new dictionary to store filtered results - filtered_dict = {} - - # Loop through each key-value pair in the 'Packages' dictionary - for key, value in repo_data.items(): - # If the key contains the desired substring, add it to the filtered dictionary - if substring in key: - filtered_dict[key] = value - - return filtered_dict - - def _patch_repodata(repodata, subdir): index = repodata["packages"] instructions = { diff --git a/numpy2.py b/numpy2.py index 3a85348..825ee28 100644 --- a/numpy2.py +++ b/numpy2.py @@ -26,16 +26,11 @@ CHANNEL_ALIAS = "https://repo.anaconda.com/pkgs" SUBDIRS = ( "noarch", - "linux-32", "linux-64", "linux-aarch64", - "linux-armv6l", - "linux-armv7l", - "linux-ppc64le", "linux-s390x", "osx-64", "osx-arm64", - "win-32", "win-64", ) From d75edb5e07319f2f2a5eed90da7d528ac85a5a59 Mon Sep 17 00:00:00 2001 From: James Robertson Date: Fri, 26 Jul 2024 10:31:42 +0100 Subject: [PATCH 29/47] Update numpy2.py Co-authored-by: Charles Bousseau <16641587+cbouss@users.noreply.github.com> --- numpy2.py | 1 + 1 file changed, 1 insertion(+) diff --git a/numpy2.py b/numpy2.py index 825ee28..06ae6b8 100644 --- a/numpy2.py +++ b/numpy2.py @@ -226,6 +226,7 @@ def main(): constrains = record.get("constrains", []) depends = [dep for dep in depends if dep is not None] + # numpy 2 is introduced for python 3.9. Packages for python 3.13 will be built with numpy2 from the start. if "py39" in fn or "py310" in fn or "py311" in fn or "py312" in fn: if name not in ["anaconda", "_anaconda_depends", "__anaconda_core_depends", "_anaconda_core"]: try: From 411223c355af69568ff1e572d1f7cba052eed5de Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Fri, 26 Jul 2024 11:12:12 +0100 Subject: [PATCH 30/47] change code for clearer changes for numpy 2 --- main.py | 55 +++---------------- numpy2.py | 2 +- ...ed_numpy_changes.json => numpy2_patch.json | 0 3 files changed, 8 insertions(+), 49 deletions(-) rename proposed_numpy_changes.json => numpy2_patch.json (100%) diff --git a/main.py b/main.py index 810ffe8..a65ddc6 100644 --- a/main.py +++ b/main.py @@ -8,7 +8,6 @@ import datetime from collections import defaultdict from os.path import dirname, isdir, isfile, join -import rattler from typing import List, Sequence from conda.models.version import VersionOrder import csv @@ -275,19 +274,19 @@ ] -def load_numpy_changes(): +def load_numpy2_changes(): try: - with open('proposed_numpy_changes.json', 'r') as f: + with open('numpy2_patch.json', 'r') as f: return json.load(f) except FileNotFoundError: - logger.warning("proposed_numpy_changes.json not found. No numpy changes will be applied.") - return {} + logger.error("numpy2_patch.json not found. Aborting hotfixes.") + sys.exit(1) -NUMPY_CHANGES = load_numpy_changes() +NUMPY_CHANGES = load_numpy2_changes() -def apply_numpy_changes(record, subdir, filename): +def apply_numpy2_changes(record, subdir, filename): """ Applies predefined numpy changes to a record based on its directory and filename. @@ -347,46 +346,6 @@ def _apply_changes_to_dependencies(depends, change, record, filename, sort_type= change['updated'], change['reason'] ]) - -async def solve_dependencies( - record: rattler.RepoDataRecord, - channels: Sequence[rattler.Channel | str], - platforms: Sequence[rattler.Platform | rattler.platform.PlatformLiteral], - virtual_packages: Sequence[rattler.GenericVirtualPackage | rattler.VirtualPackage] -) -> List[rattler.RepoDataRecord]: - # This is left in the file as it will be useful for future development - # and testing. It is not used in the current implementation. - try: - # Create a MatchSpec for the current package - name = record.name.normalized - if name == '_anaconda_depends': - return [] - version = record.version._source - build = record.build - package_spec = rattler.MatchSpec(f"{name}={version}={build}") - - # Create MatchSpecs for all dependencies - dep_specs = [rattler.MatchSpec(dep) for dep in record.depends] - - # Combine the package spec and dependency specs - all_specs = [package_spec] + dep_specs - - # Solve dependencies - solved_packages = await rattler.solve( - channels=channels, - specs=all_specs, - platforms=platforms, - virtual_packages=virtual_packages, - timeout=datetime.timedelta(seconds=10), - strategy="highest" # You can adjust this if needed - ) - logger.info(f"Solved dependencies for {name}") - return solved_packages - except Exception as exc: - logger.error(f"Failed to solve dependencies for {name}: {exc}") - return [] - - def write_csv(): """ Writes update data to CSV files in the 'updates' directory. @@ -814,7 +773,7 @@ def patch_record_in_place(fn, record, subdir): break if NUMPY_CHANGES is not {}: - apply_numpy_changes(record, subdir, fn) + apply_numpy2_changes(record, subdir, fn) ########### # pytorch # diff --git a/numpy2.py b/numpy2.py index 06ae6b8..d8090b2 100644 --- a/numpy2.py +++ b/numpy2.py @@ -240,7 +240,7 @@ def main(): logger.error(f"numpy 2.0.0 error {fn}: {e}") # Write proposed changes to a JSON file - json_filename = "proposed_numpy_changes.json" + json_filename = "numpy2_patch.json" with open(json_filename, 'w') as f: json.dump(proposed_changes, f, indent=2) diff --git a/proposed_numpy_changes.json b/numpy2_patch.json similarity index 100% rename from proposed_numpy_changes.json rename to numpy2_patch.json From 6716a8f7726a714c9390f24ce5b07dfae1888a57 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Fri, 26 Jul 2024 11:12:50 +0100 Subject: [PATCH 31/47] remove rattler goodness --- .github/workflows/ci.yml | 2 +- README.md | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f061e17..e56670d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,7 +19,7 @@ jobs: - name: Setup environment shell: bash -l {0} run: | - conda create --name testenv conda conda-index flake8 requests conda-forge::py-rattler + conda create --name testenv conda conda-index flake8 requests - name: Lint shell: bash -l {0} run: | diff --git a/README.md b/README.md index 0adc229..c671963 100644 --- a/README.md +++ b/README.md @@ -61,7 +61,7 @@ python numpy2.py 1. Scans through the repodata for packages depending on numpy. 2. Checks if these dependencies need updates to ensure compatibility with numpy 2.0. 3. Proposes changes to add upper bounds to numpy dependencies where necessary. -4. Generates a `proposed_numpy_changes.json` file containing all proposed changes. +4. Generates a `numpy2_patch.json` file containing all proposed changes. ### When to use numpy2.py @@ -72,16 +72,16 @@ Use `numpy2.py` when: ### Running main.py with proposed_numpy_changes.json -After running `numpy2.py`, you'll have a `proposed_numpy_changes.json` file. To apply these changes: +After running `numpy2.py`, you'll have a `numpy2_patch.json` file. To apply these changes: -1. Ensure `proposed_numpy_changes.json` is in the same directory as `main.py`. +1. Ensure `numpy2_patch.json` is in the same directory as `main.py`. 2. Run `main.py` as usual: ``` python main.py ``` -`main.py` will automatically detect and incorporate the changes from `proposed_numpy_changes.json` into the hotfix process. +`main.py` will automatically detect and incorporate the changes from `numpy2_patch.json` into the hotfix process. ## Reviewing CSV Updates From 8dd4c112abc0a536d1dae14fc2e1dd7209a6444e Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Fri, 26 Jul 2024 11:17:30 +0100 Subject: [PATCH 32/47] change to n2 --- main.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/main.py b/main.py index a65ddc6..ed1703b 100644 --- a/main.py +++ b/main.py @@ -283,7 +283,7 @@ def load_numpy2_changes(): sys.exit(1) -NUMPY_CHANGES = load_numpy2_changes() +NUMPY_2_CHANGES = load_numpy2_changes() def apply_numpy2_changes(record, subdir, filename): @@ -295,9 +295,9 @@ def apply_numpy2_changes(record, subdir, filename): - subdir: The subdirectory of the record. - filename: The filename of the record. """ - if subdir not in NUMPY_CHANGES or filename not in NUMPY_CHANGES[subdir]: + if subdir not in NUMPY_2_CHANGES or filename not in NUMPY_2_CHANGES[subdir]: return - changes = NUMPY_CHANGES[subdir][filename] + changes = NUMPY_2_CHANGES[subdir][filename] for change in changes: depends = _get_dependency_list(record, change['type']) if depends is None: @@ -772,7 +772,7 @@ def patch_record_in_place(fn, record, subdir): depends[i] = depends[i].replace(">=1.21.5,", ">=1.21.2,") break - if NUMPY_CHANGES is not {}: + if NUMPY_2_CHANGES is not {}: apply_numpy2_changes(record, subdir, fn) ########### @@ -1636,7 +1636,7 @@ def do_hotfixes(base_dir): def main(): base_dir = join(dirname(__file__), CHANNEL_NAME) do_hotfixes(base_dir) - if NUMPY_CHANGES != {}: + if NUMPY_2_CHANGES != {}: write_csv() From c896b1b2bffb78661b39fed604238a48f078aadc Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Fri, 26 Jul 2024 11:28:12 +0100 Subject: [PATCH 33/47] flake8 --- main.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/main.py b/main.py index ed1703b..20a5752 100644 --- a/main.py +++ b/main.py @@ -5,10 +5,8 @@ import os import re import sys -import datetime from collections import defaultdict from os.path import dirname, isdir, isfile, join -from typing import List, Sequence from conda.models.version import VersionOrder import csv import requests @@ -346,6 +344,7 @@ def _apply_changes_to_dependencies(depends, change, record, filename, sort_type= change['updated'], change['reason'] ]) + def write_csv(): """ Writes update data to CSV files in the 'updates' directory. From d2ab4c98bebfe01cab637cf1fa2c553eaac799d6 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Fri, 26 Jul 2024 17:43:42 +0100 Subject: [PATCH 34/47] remove logging for items not being updated --- numpy2.py | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/numpy2.py b/numpy2.py index d8090b2..a777617 100644 --- a/numpy2.py +++ b/numpy2.py @@ -168,28 +168,16 @@ def update_numpy_dependencies(dependencies_list, package_record, dependency_type new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Version comparison failed") - else: - collect_proposed_change(package_subdir, filename, dependency_type, dependency, - dependency, "Missing version or protected_version") elif numpy2_protect_dict.get('add_bound_to_unspecified', False): if len(parts) > 1: new_dependency = patch_record_with_fixed_deps(dependency, parts) if new_dependency != dependency: collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Upper bound added") - else: - collect_proposed_change(package_subdir, filename, dependency_type, dependency, - dependency, "No unspecified bound") else: new_dependency = f"{dependency} <2.0a0" collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Upper bound added") - else: - collect_proposed_change(package_subdir, filename, dependency_type, dependency, - dependency, "Not in protect_dict, no unspecified bound") - else: - collect_proposed_change(package_subdir, filename, dependency_type, dependency, - dependency, "Already has upper bound") def main(): From 2d59ddb6e4361b1290d1d3b30514bd4c4dcf75ad Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Fri, 26 Jul 2024 17:44:10 +0100 Subject: [PATCH 35/47] regenerate n2 patch --- numpy2_patch.json | 107248 ++++++++----------------------------------- 1 file changed, 18324 insertions(+), 88924 deletions(-) diff --git a/numpy2_patch.json b/numpy2_patch.json index a96afcf..0e7189d 100644 --- a/numpy2_patch.json +++ b/numpy2_patch.json @@ -1,53 +1,5 @@ { "linux-64": { - 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} - ], - "zfpy-1.0.0-py311hf62ec03_0.tar.bz2": [ - { - "type": "dep", - "original": "numpy >=1.23.5,<2.0a0", - "updated": "numpy >=1.23.5,<2.0a0", - "reason": "Already has upper bound" - } - ], - "zfpy-1.0.0-py39hf11a4ad_0.tar.bz2": [ - { - "type": "dep", - "original": "numpy >=1.16.6,<2.0a0", - "updated": "numpy >=1.16.6,<2.0a0", - "reason": "Already has upper bound" - } ] } } \ No newline at end of file From c1b77955ca4774a459478704019f82dae88eb1af Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 1 Aug 2024 08:53:17 +0100 Subject: [PATCH 36/47] make changes suggested in previous review --- numpy2.py => generate_numpy2_patch.py | 46 +- main.py | 83 +- numpy2_patch.json | 82215 +++++++++++------------- tests/test_numpy.py | 62 + 4 files changed, 38601 insertions(+), 43805 deletions(-) rename numpy2.py => generate_numpy2_patch.py (86%) create mode 100644 tests/test_numpy.py diff --git a/numpy2.py b/generate_numpy2_patch.py similarity index 86% rename from numpy2.py rename to generate_numpy2_patch.py index a777617..6f5eb92 100644 --- a/numpy2.py +++ b/generate_numpy2_patch.py @@ -1,24 +1,26 @@ from os.path import dirname, isdir, isfile, join from conda.models.version import VersionOrder -import csv from collections import defaultdict import requests -from numpy2_config import numpy2_protect_dict import logging import json import os import re -proposed_changes = defaultdict(lambda: defaultdict(list)) +numpy2_protect_dict = { + 'add_bound_to_unspecified': True, + 'pandas': '2.2.2', + 'scikit-learn': '1.4.2', + 'pyamg': '4.2.3', + 'pyqtgraph': '0.13.1' +} -# Global dictionary to store data for CSV output -csv_data = defaultdict(list) +proposed_changes = [] # Configure the logging logging.basicConfig(level=logging.DEBUG, - format='%(asctime)s - %(name)s - %(levelname)s - %(message)s', - handlers=[logging.FileHandler('hotfixes.log', mode='w'), - logging.StreamHandler()]) + format='%(asctime)s - %(name)s - %(levelname)s - %(message)s') + # Create a logger object logger = logging.getLogger(__name__) @@ -47,13 +49,17 @@ def collect_proposed_change(subdirectory, filename, change_type, original_depend - updated_dependency: The updated dependency string. - reason: The reason for the change. """ - proposed_changes[subdirectory][filename].append({ + proposed_changes.append({ + "subdirectory": subdirectory, + "filename": filename, "type": change_type, "original": original_dependency, "updated": updated_dependency, - "reason": reason }) + logger.info(f"numpy 2.0.0: {reason} for {filename}. " + f"Original: '{original_dependency}' -> New: '{updated_dependency}' ({reason})") + def parse_version(version_str): """ @@ -117,26 +123,6 @@ def write_csv(): writer.writerows(data) -def log_and_collect(issue_type, package_info, original_dependency, updated_dependency, reason): - """ - Logs and collects data on dependency modifications for reporting. - - Parameters: - - issue_type: Type of issue prompting modification. - - package_info: Package name, version, build, and build number. - - original_dependency: Original dependency specification. - - updated_dependency: Updated dependency specification. - - reason: Reason for modification. - """ - logger.info(f"numpy 2.0.0: {issue_type} for {package_info}. " - f"Original: '{original_dependency}' -> New: '{updated_dependency}' ({reason})") - - name, version = package_info.split(' v')[0], package_info.split(' v')[1].split(' (')[0] - build = package_info.split('build: ')[1].split(',')[0] - build_number = package_info.split('build_number: ')[1][:-1] - csv_data[issue_type].append([name, version, build, build_number, original_dependency, updated_dependency, reason]) - - def update_numpy_dependencies(dependencies_list, package_record, dependency_type, package_subdir, filename): """ Adds upper bounds to numpy dependencies as needed. diff --git a/main.py b/main.py index 389c406..4401d8b 100644 --- a/main.py +++ b/main.py @@ -5,23 +5,12 @@ import os import re import sys +import requests from collections import defaultdict from os.path import dirname, isdir, isfile, join from conda.models.version import VersionOrder -import csv -import requests -import logging +from pathlib import Path -# Global dictionary to store data for CSV output -csv_data = defaultdict(list) - -# Configure the logging -logging.basicConfig(level=logging.DEBUG, - format='%(asctime)s - %(name)s - %(levelname)s - %(message)s', - handlers=[logging.FileHandler('hotfixes.log', mode='w'), - logging.StreamHandler()]) -# Create a logger object -logger = logging.getLogger(__name__) CHANNEL_NAME = "main" CHANNEL_ALIAS = "https://repo.anaconda.com/pkgs" @@ -284,16 +273,8 @@ ] -def load_numpy2_changes(): - try: - with open('numpy2_patch.json', 'r') as f: - return json.load(f) - except FileNotFoundError: - logger.error("numpy2_patch.json not found. Aborting hotfixes.") - sys.exit(1) - -NUMPY_2_CHANGES = load_numpy2_changes() +NUMPY_2_CHANGES = json.loads(Path("numpy2_patch.json").read_text()) def apply_numpy2_changes(record, subdir, filename): @@ -305,14 +286,19 @@ def apply_numpy2_changes(record, subdir, filename): - subdir: The subdirectory of the record. - filename: The filename of the record. """ - if subdir not in NUMPY_2_CHANGES or filename not in NUMPY_2_CHANGES[subdir]: + relevant_changes = [ + change for change in NUMPY_2_CHANGES + if change['subdirectory'] == subdir and change['filename'] == filename + ] + + if not relevant_changes: return - changes = NUMPY_2_CHANGES[subdir][filename] - for change in changes: + + for change in relevant_changes: depends = _get_dependency_list(record, change['type']) if depends is None: continue - _apply_changes_to_dependencies(depends, change, record, filename, 'type') + replace_dep(depends, change["original"], change["updated"]) def _get_dependency_list(record, change_type): @@ -333,46 +319,6 @@ def _get_dependency_list(record, change_type): return None -def _apply_changes_to_dependencies(depends, change, record, filename, sort_type='reason'): - """ - Applies changes to dependencies and logs the changes. - - Parameters: - - depends (list): The list of dependencies to be modified. - - change (dict): A dict containing the original dependency, the updated dependency, the reason for the change. - - record (dict): The record to which the changes apply. - - filename (str): The name of the file being processed. - - sort_type (str, optional): The key in the 'change' dictionary to sort the CSV data by. Defaults to 'reason'. - """ - for i, dep in enumerate(depends): - if dep == change['original']: - depends[i] = change['updated'] - if change['reason'] == 'Upper bound added': - logger.info(f"Applied numpy change for {filename}: {change['original']} -> {change['updated']}") - # Add to csv_data for later CSV export - csv_data[change[sort_type]].append([ - record['name'], record['version'], record['build'], - record['build_number'], change['original'], - change['updated'], change['reason'] - ]) - - -def write_csv(): - """ - Writes update data to CSV files in the 'updates' directory. - """ - if not os.path.exists("updates"): - os.makedirs("updates") - - for issue_type, data in csv_data.items(): - with open(f"updates/{issue_type}_numpy2_updates.csv", 'w', newline='') as csvfile: - csv.writer(csvfile).writerow(['Package', 'Version', - 'Build', 'Build Number', - 'Original Dependency', 'Updated Dependency', - 'Reason']) - csv.writer(csvfile).writerows(data) - - def _replace_vc_features_with_vc_pkg_deps(name, record, depends): python_vc_deps = { "2.6": "vc 9.*", @@ -786,7 +732,7 @@ def patch_record_in_place(fn, record, subdir): depends[i] = depends[i].replace(">=1.21.5,", ">=1.21.2,") break - if NUMPY_2_CHANGES is not {}: + if NUMPY_2_CHANGES: apply_numpy2_changes(record, subdir, fn) ########### @@ -1671,7 +1617,8 @@ def main(): base_dir = join(dirname(__file__), CHANNEL_NAME) do_hotfixes(base_dir) if NUMPY_2_CHANGES != {}: - write_csv() + # write_csv() + pass if __name__ == "__main__": diff --git a/numpy2_patch.json b/numpy2_patch.json index 0e7189d..07266de 100644 --- a/numpy2_patch.json +++ b/numpy2_patch.json @@ -1,43708 +1,38509 @@ -{ - "linux-64": { - "altair-4.2.2-py310h06a4308_0.tar.bz2": [ - { - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0", - "reason": "Upper bound added" - } - ], - "altair-4.2.2-py311h06a4308_0.tar.bz2": [ - { - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0", - "reason": "Upper 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"yt-4.1.4-py39hf11a4ad_0.tar.bz2", + "type": "dep", + "original": "numpy >=1.14.5", + "updated": "numpy >=1.14.5,<2.0a0" + }, + { + "subdirectory": "win-64", + "filename": "zarr-2.13.3-py310haa95532_0.tar.bz2", + "type": "dep", + "original": "numpy >=1.7", + "updated": "numpy >=1.7,<2.0a0" + }, + { + "subdirectory": "win-64", + "filename": "zarr-2.13.3-py311haa95532_0.tar.bz2", + "type": "dep", + "original": "numpy >=1.7", + "updated": "numpy >=1.7,<2.0a0" + }, + { + "subdirectory": "win-64", + "filename": "zarr-2.13.3-py312haa95532_0.tar.bz2", + "type": "dep", + "original": "numpy >=1.7", + "updated": "numpy >=1.7,<2.0a0" + }, + { + "subdirectory": "win-64", + "filename": "zarr-2.13.3-py39haa95532_0.tar.bz2", + "type": "dep", + "original": "numpy >=1.7", + "updated": "numpy >=1.7,<2.0a0" } -} \ No newline at end of file +] \ No newline at end of file diff --git a/tests/test_numpy.py b/tests/test_numpy.py new file mode 100644 index 0000000..833c84a --- /dev/null +++ b/tests/test_numpy.py @@ -0,0 +1,62 @@ +from main import SUBDIRS +import json +import os +import pytest + +@pytest.fixture +def json_data(): + """Fixture to load the JSON data from the output file.""" + json_file = 'numpy2_patch.json' + if not os.path.exists(json_file): + pytest.skip(f"{json_file} not found in {os.getcwd()}. Run the main script first.") + with open(json_file, 'r') as f: + return json.load(f) + +def test_json_structure(json_data): + """Test the overall structure of the JSON output.""" + assert isinstance(json_data, list), "JSON root should be a list" + assert len(json_data) > 0, "JSON should not be empty" + + for item in json_data: + assert isinstance(item, dict), "Each item in the JSON should be a dictionary" + assert set(item.keys()) == {'subdirectory', 'filename', 'type', 'original', 'updated'}, \ + f"Item has incorrect keys: {item.keys()}" + assert item['subdirectory'] in SUBDIRS, f"Unexpected subdir {item['subdirectory']} in the JSON output" + + # Log which subdirs are missing + present_subdirs = set(item['subdirectory'] for item in json_data) + missing_subdirs = set(SUBDIRS) - present_subdirs + if missing_subdirs: + print(f"Note: The following subdirs are not present in the JSON output: {', '.join(missing_subdirs)}") + +def test_change_types(json_data): + """Test that change types are either 'dep' or 'constr'.""" + valid_types = {'dep', 'constr'} + for item in json_data: + assert item['type'] in valid_types, \ + f"Invalid change type for {item['filename']} in {item['subdirectory']}: {item['type']}" + +def test_numpy_changes(json_data): + """Test that changes are related to numpy or numpy-base.""" + for item in json_data: + assert 'numpy' in item['original'].lower() or 'numpy-base' in item['original'].lower(), \ + f"Change for {item['filename']} in {item['subdirectory']} is not related to numpy: {item['original']}" + +def test_version_bounds(json_data): + """Test that updated dependencies have the correct version bounds.""" + for item in json_data: + if item['original'] != item['updated']: + assert '<2.0a0' in item['updated'], ( + f"Updated dependency for {item['filename']} in {item['subdirectory']} " + f"doesn't have correct upper bound: {item['updated']}" + ) + +def test_changes_present(json_data): + """Test that there are actually changes in the output.""" + assert json_data, "JSON output should not be empty" + assert len(set(item['subdirectory'] for item in json_data)) > 0, "At least one subdir should have changes" + +def test_changes_present(json_data): + """Test that there are actually changes in the output.""" + assert json_data, "JSON output should not be empty" + assert len(set(item['subdirectory'] for item in json_data)) > 0, "At least one subdir should have changes" \ No newline at end of file From 7639c1a1f845522a3563ed46994d9f7eba90ee48 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 1 Aug 2024 08:58:26 +0100 Subject: [PATCH 37/47] linting errors fixed --- main.py | 10 ++--- test_numpy.py | 99 --------------------------------------------- tests/test_numpy.py | 11 ++--- 3 files changed, 9 insertions(+), 111 deletions(-) delete mode 100644 test_numpy.py diff --git a/main.py b/main.py index 4401d8b..786362b 100644 --- a/main.py +++ b/main.py @@ -273,7 +273,6 @@ ] - NUMPY_2_CHANGES = json.loads(Path("numpy2_patch.json").read_text()) @@ -287,13 +286,13 @@ def apply_numpy2_changes(record, subdir, filename): - filename: The filename of the record. """ relevant_changes = [ - change for change in NUMPY_2_CHANGES + change for change in NUMPY_2_CHANGES if change['subdirectory'] == subdir and change['filename'] == filename ] - + if not relevant_changes: return - + for change in relevant_changes: depends = _get_dependency_list(record, change['type']) if depends is None: @@ -1616,9 +1615,6 @@ def do_hotfixes(base_dir): def main(): base_dir = join(dirname(__file__), CHANNEL_NAME) do_hotfixes(base_dir) - if NUMPY_2_CHANGES != {}: - # write_csv() - pass if __name__ == "__main__": diff --git a/test_numpy.py b/test_numpy.py deleted file mode 100644 index bf248f9..0000000 --- a/test_numpy.py +++ /dev/null @@ -1,99 +0,0 @@ -from main import SUBDIRS # Import SUBDIRS from your main script - -import json -import os -import pytest - - -@pytest.fixture -def json_data(): - """Fixture to load the JSON data from the output file.""" - json_file = 'proposed_numpy_changes.json' - if not os.path.exists(json_file): - pytest.skip(f"{json_file} not found. Run the main script first.") - with open(json_file, 'r') as f: - return json.load(f) - - -def test_json_structure(json_data): - """Test the overall structure of the JSON output.""" - assert isinstance(json_data, dict), "JSON root should be a dictionary" - - # Check if at least one subdir is present - assert any(subdir in json_data for subdir in SUBDIRS), "At least one subdir should be in the JSON output" - - for subdir in json_data: - assert subdir in SUBDIRS, f"Unexpected subdir {subdir} in the JSON output" - assert isinstance(json_data[subdir], dict), f"Subdir {subdir} should contain a dictionary" - - # Log which subdirs are missing - missing_subdirs = [subdir for subdir in SUBDIRS if subdir not in json_data] - if missing_subdirs: - print(f"Note: The following subdirs are not present in the JSON output: {', '.join(missing_subdirs)}") - - -def test_package_structure(json_data): - """Test the structure of each package entry.""" - for subdir, packages in json_data.items(): - for package, changes in packages.items(): - assert isinstance(changes, list), f"Changes for {package} in {subdir} should be a list" - for change in changes: - assert isinstance(change, dict), f"Each change for {package} in {subdir} should be a dictionary" - assert set(change.keys()) == {'type', 'original', 'updated', 'reason'}, \ - f"Change for {package} in {subdir} has incorrect keys" - - -def test_change_types(json_data): - """Test that change types are either 'dep' or 'constr'.""" - valid_types = {'dep', 'constr'} - for subdir, packages in json_data.items(): - for package, changes in packages.items(): - for change in changes: - assert change['type'] in valid_types, \ - f"Invalid change type for {package} in {subdir}: {change['type']}" - - -def test_numpy_changes(json_data): - """Test that changes are related to numpy or numpy-base.""" - for subdir, packages in json_data.items(): - for package, changes in packages.items(): - for change in changes: - assert 'numpy' in change['original'].lower() or 'numpy-base' in change['original'].lower(), \ - f"Change for {package} in {subdir} is not related to numpy: {change['original']}" - - -def test_version_bounds(json_data): - """Test that updated dependencies have the correct version bounds.""" - for subdir, packages in json_data.items(): - for package, changes in packages.items(): - for change in changes: - if change['original'] != change['updated']: - assert '<2.0a0' in change['updated'], ( - f"Updated dependency for {package} in {subdir} " - f"doesn't have correct upper bound: {change['updated']}" - ) - - -def test_reason_provided(json_data): - """Test that each change has a non-empty reason.""" - for subdir, packages in json_data.items(): - for package, changes in packages.items(): - for change in changes: - assert change['reason'], f"Change for {package} in {subdir} has no reason provided" - - -def test_no_empty_changes(json_data): - """Test that there are no packages with empty change lists.""" - for subdir, packages in json_data.items(): - for package, changes in packages.items(): - assert changes, f"Package {package} in {subdir} has no changes" - - -def test_changes_present(json_data): - """Test that there are actually changes in the output.""" - assert json_data, "JSON output should not be empty" - assert any(packages for packages in json_data.values()), "At least one subdir should have changes" - - -if __name__ == '__main__': - pytest.main([__file__]) diff --git a/tests/test_numpy.py b/tests/test_numpy.py index 833c84a..9f461d5 100644 --- a/tests/test_numpy.py +++ b/tests/test_numpy.py @@ -3,6 +3,7 @@ import os import pytest + @pytest.fixture def json_data(): """Fixture to load the JSON data from the output file.""" @@ -12,6 +13,7 @@ def json_data(): with open(json_file, 'r') as f: return json.load(f) + def test_json_structure(json_data): """Test the overall structure of the JSON output.""" assert isinstance(json_data, list), "JSON root should be a list" @@ -29,6 +31,7 @@ def test_json_structure(json_data): if missing_subdirs: print(f"Note: The following subdirs are not present in the JSON output: {', '.join(missing_subdirs)}") + def test_change_types(json_data): """Test that change types are either 'dep' or 'constr'.""" valid_types = {'dep', 'constr'} @@ -36,12 +39,14 @@ def test_change_types(json_data): assert item['type'] in valid_types, \ f"Invalid change type for {item['filename']} in {item['subdirectory']}: {item['type']}" + def test_numpy_changes(json_data): """Test that changes are related to numpy or numpy-base.""" for item in json_data: assert 'numpy' in item['original'].lower() or 'numpy-base' in item['original'].lower(), \ f"Change for {item['filename']} in {item['subdirectory']} is not related to numpy: {item['original']}" + def test_version_bounds(json_data): """Test that updated dependencies have the correct version bounds.""" for item in json_data: @@ -51,12 +56,8 @@ def test_version_bounds(json_data): f"doesn't have correct upper bound: {item['updated']}" ) -def test_changes_present(json_data): - """Test that there are actually changes in the output.""" - assert json_data, "JSON output should not be empty" - assert len(set(item['subdirectory'] for item in json_data)) > 0, "At least one subdir should have changes" def test_changes_present(json_data): """Test that there are actually changes in the output.""" assert json_data, "JSON output should not be empty" - assert len(set(item['subdirectory'] for item in json_data)) > 0, "At least one subdir should have changes" \ No newline at end of file + assert len(set(item['subdirectory'] for item in json_data)) > 0, "At least one subdir should have changes" From c09fa2ff49e32b06780fc58451c40c5b99ef1a65 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 1 Aug 2024 09:00:04 +0100 Subject: [PATCH 38/47] delete numpy2 config and lint modifications --- generate_numpy2_patch.py | 18 ++---------------- numpy2_config.py | 8 -------- 2 files changed, 2 insertions(+), 24 deletions(-) delete mode 100644 numpy2_config.py diff --git a/generate_numpy2_patch.py b/generate_numpy2_patch.py index 6f5eb92..57791aa 100644 --- a/generate_numpy2_patch.py +++ b/generate_numpy2_patch.py @@ -1,6 +1,5 @@ from os.path import dirname, isdir, isfile, join from conda.models.version import VersionOrder -from collections import defaultdict import requests import logging import json @@ -50,7 +49,7 @@ def collect_proposed_change(subdirectory, filename, change_type, original_depend - reason: The reason for the change. """ proposed_changes.append({ - "subdirectory": subdirectory, + "subdirectory": subdirectory, "filename": filename, "type": change_type, "original": original_dependency, @@ -110,19 +109,6 @@ def patch_record_with_fixed_deps(dependency, parts): return dependency -def write_csv(): - """ - Writes collected data to CSV files, one per issue type. - """ - for issue_type, data in csv_data.items(): - filename = f"{issue_type}_numpy2_updates.csv" - with open(filename, 'w', newline='') as csvfile: - writer = csv.writer(csvfile) - writer.writerow(['Package', 'Version', 'Build', 'Build Number', - 'Original Dependency', 'Updated Dependency', 'Reason']) - writer.writerows(data) - - def update_numpy_dependencies(dependencies_list, package_record, dependency_type, package_subdir, filename): """ Adds upper bounds to numpy dependencies as needed. @@ -135,7 +121,7 @@ def update_numpy_dependencies(dependencies_list, package_record, dependency_type - package_subdir: Package location subdirectory. - filename: Package filename. """ - for i, dependency in enumerate(dependencies_list): + for _, dependency in enumerate(dependencies_list): parts = dependency.split() package_name = parts[0] if package_name in ["numpy", "numpy-base"]: diff --git a/numpy2_config.py b/numpy2_config.py deleted file mode 100644 index be1389e..0000000 --- a/numpy2_config.py +++ /dev/null @@ -1,8 +0,0 @@ -numpy2_protect_dict = { - 'add_bound_to_unspecified': True, - 'pandas': '2.2.2', - 'scikit-learn': '1.4.2', - 'pyamg': '4.2.3', - 'pyqtgraph': '0.13.1' - # Add more packages as needed -} From 4326c27cf336fb22441ca4d515c57c9c19d1ad48 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 1 Aug 2024 20:41:27 +0100 Subject: [PATCH 39/47] speed up patching process with better data handling --- generate_numpy2_patch.py | 58 +- main.py | 56 +- numpy2_patch.json | 65561 +++++++++++++++---------------------- 3 files changed, 27103 insertions(+), 38572 deletions(-) diff --git a/generate_numpy2_patch.py b/generate_numpy2_patch.py index 57791aa..3852ca2 100644 --- a/generate_numpy2_patch.py +++ b/generate_numpy2_patch.py @@ -1,13 +1,12 @@ -from os.path import dirname, isdir, isfile, join -from conda.models.version import VersionOrder import requests import logging import json -import os import re +from collections import defaultdict +from pathlib import Path +from conda.models.version import VersionOrder numpy2_protect_dict = { - 'add_bound_to_unspecified': True, 'pandas': '2.2.2', 'scikit-learn': '1.4.2', 'pyamg': '4.2.3', @@ -36,6 +35,10 @@ ) +# Initialize NUMPY_2_CHANGES with a nested defaultdict structure +NUMPY_2_CHANGES = defaultdict(lambda: defaultdict(dict)) + + def collect_proposed_change(subdirectory, filename, change_type, original_dependency, updated_dependency, reason): """ Collects a proposed change to a dependency for later processing. @@ -43,18 +46,22 @@ def collect_proposed_change(subdirectory, filename, change_type, original_depend Parameters: - subdirectory: The subdirectory where the file is located. - filename: The name of the file being modified. - - change_type: The type of change (e.g., 'version update'). + - change_type: The type of change (e.g., 'dep', 'constr'). - original_dependency: The original dependency string. - updated_dependency: The updated dependency string. - reason: The reason for the change. """ - proposed_changes.append({ - "subdirectory": subdirectory, - "filename": filename, + # change dep and constr to dependency and constraint + if change_type == "dep": + change_type = "depends" + elif change_type == "constr": + change_type = "constrains" + + NUMPY_2_CHANGES[subdirectory][filename] = { "type": change_type, "original": original_dependency, - "updated": updated_dependency, - }) + "updated": updated_dependency + } logger.info(f"numpy 2.0.0: {reason} for {filename}. " f"Original: '{original_dependency}' -> New: '{updated_dependency}' ({reason})") @@ -121,6 +128,7 @@ def update_numpy_dependencies(dependencies_list, package_record, dependency_type - package_subdir: Package location subdirectory. - filename: Package filename. """ + add_bound_to_unspecified = True for _, dependency in enumerate(dependencies_list): parts = dependency.split() package_name = parts[0] @@ -140,7 +148,7 @@ def update_numpy_dependencies(dependencies_list, package_record, dependency_type new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Version comparison failed") - elif numpy2_protect_dict.get('add_bound_to_unspecified', False): + elif add_bound_to_unspecified: if len(parts) > 1: new_dependency = patch_record_with_fixed_deps(dependency, parts) if new_dependency != dependency: @@ -153,24 +161,20 @@ def update_numpy_dependencies(dependencies_list, package_record, dependency_type def main(): - base_dir = join(dirname(__file__), CHANNEL_NAME) - # Step 1. Collect initial repodata for all subdirs. + base_dir = Path(__file__).parent / CHANNEL_NAME repodatas = {} for subdir in SUBDIRS: - repodata_path = join(base_dir, subdir, "repodata_from_packages.json") - if isfile(repodata_path): - with open(repodata_path) as fh: + repodata_path = base_dir / subdir / "repodata_from_packages.json" + if repodata_path.is_file(): + with repodata_path.open() as fh: repodatas[subdir] = json.load(fh) else: - repodata_url = "/".join( - (CHANNEL_ALIAS, CHANNEL_NAME, subdir, "repodata_from_packages.json") - ) + repodata_url = f"{CHANNEL_ALIAS}/{CHANNEL_NAME}/{subdir}/repodata_from_packages.json" response = requests.get(repodata_url) response.raise_for_status() repodatas[subdir] = response.json() - if not isdir(dirname(repodata_path)): - os.makedirs(dirname(repodata_path)) - with open(repodata_path, "w") as fh: + repodata_path.parent.mkdir(parents=True, exist_ok=True) + with repodata_path.open('w') as fh: json.dump( repodatas[subdir], fh, @@ -186,8 +190,7 @@ def main(): constrains = record.get("constrains", []) depends = [dep for dep in depends if dep is not None] - # numpy 2 is introduced for python 3.9. Packages for python 3.13 will be built with numpy2 from the start. - if "py39" in fn or "py310" in fn or "py311" in fn or "py312" in fn: + if any(py_ver in fn for py_ver in ["py39", "py310", "py311", "py312"]): if name not in ["anaconda", "_anaconda_depends", "__anaconda_core_depends", "_anaconda_core"]: try: for dep in depends: @@ -199,10 +202,9 @@ def main(): except Exception as e: logger.error(f"numpy 2.0.0 error {fn}: {e}") - # Write proposed changes to a JSON file - json_filename = "numpy2_patch.json" - with open(json_filename, 'w') as f: - json.dump(proposed_changes, f, indent=2) + json_filename = Path("numpy2_patch.json") + with json_filename.open('w') as f: + json.dump(dict(NUMPY_2_CHANGES), f, indent=2) logger.info(f"Proposed changes have been written to {json_filename}") diff --git a/main.py b/main.py index 786362b..8485fa3 100644 --- a/main.py +++ b/main.py @@ -3,14 +3,14 @@ import fnmatch import json import os +from os.path import dirname, isdir, isfile, join import re import sys -import requests from collections import defaultdict -from os.path import dirname, isdir, isfile, join -from conda.models.version import VersionOrder from pathlib import Path +from conda.models.version import VersionOrder +import requests CHANNEL_NAME = "main" CHANNEL_ALIAS = "https://repo.anaconda.com/pkgs" @@ -279,43 +279,22 @@ def apply_numpy2_changes(record, subdir, filename): """ Applies predefined numpy changes to a record based on its directory and filename. - Parameters: - record: The record to update. - subdir: The subdirectory of the record. - filename: The filename of the record. """ - relevant_changes = [ - change for change in NUMPY_2_CHANGES - if change['subdirectory'] == subdir and change['filename'] == filename - ] - - if not relevant_changes: + if subdir not in NUMPY_2_CHANGES: return - for change in relevant_changes: - depends = _get_dependency_list(record, change['type']) - if depends is None: - continue - replace_dep(depends, change["original"], change["updated"]) - - -def _get_dependency_list(record, change_type): - """ - Returns the appropriate dependency list based on the change type. - - Parameters: - - record (dict): The record containing dependency information. - - change_type (str): The type of change ('dep' for dependencies, 'constr' for constraints). - - Returns: - - list: The list of dependencies or constraints based on the change type, None if the change type is unrecognized. - """ - if change_type == 'dep': - return record['depends'] - elif change_type == 'constr': - return record.get('constrains', []) - return None + change = NUMPY_2_CHANGES[subdir].get(filename) + if not change: + return + else: + try: + replace_dep(record[change["type"]], change["original"], change["updated"]) + except KeyError: + pass def _replace_vc_features_with_vc_pkg_deps(name, record, depends): @@ -731,9 +710,6 @@ def patch_record_in_place(fn, record, subdir): depends[i] = depends[i].replace(">=1.21.5,", ">=1.21.2,") break - if NUMPY_2_CHANGES: - apply_numpy2_changes(record, subdir, fn) - ########### # pytorch # ########### @@ -1490,6 +1466,14 @@ def patch_record_in_place(fn, record, subdir): if name == "clangxx_osx-64" and version == "4.0.1" and int(build_number) < 17: depends[:] = ["clang_osx-64 >=4.0.1,<4.0.2.0a0", "clangxx", "libcxx"] + ########### + # numpy 2 # + ########### + + # Numpy 2.0.0 Patch + if NUMPY_2_CHANGES: + apply_numpy2_changes(record, subdir, fn) + def replace_dep(depends, old, new, *, append=False): """ diff --git a/numpy2_patch.json b/numpy2_patch.json index 07266de..9856dd5 100644 --- a/numpy2_patch.json +++ b/numpy2_patch.json @@ -1,38509 +1,27054 @@ -[ - { - "subdirectory": "linux-64", - "filename": "altair-4.2.2-py310h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "altair-4.2.2-py311h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "altair-4.2.2-py39h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "altair-5.0.1-py310h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "altair-5.0.1-py311h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "altair-5.0.1-py312h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "altair-5.0.1-py39h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "arviz-0.16.0-py310h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy >=1.21.0", - "updated": "numpy >=1.21.0,<2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "arviz-0.16.0-py311h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy >=1.21.0", - "updated": "numpy >=1.21.0,<2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "arviz-0.16.0-py312h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy >=1.21.0", - "updated": "numpy >=1.21.0,<2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "arviz-0.16.0-py39h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy >=1.21.0", - "updated": "numpy >=1.21.0,<2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "astropy-4.2.1-py39h27cfd23_1.tar.bz2", - "type": "dep", - "original": "numpy >=1.17", - "updated": "numpy >=1.17,<2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "astropy-4.3.post1-py39h7f8727e_1.tar.bz2", - "type": "dep", - "original": "numpy >=1.17", - "updated": "numpy >=1.17,<2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "autograd-1.5-py310h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy >=1.12", - "updated": "numpy >=1.12,<2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "autograd-1.5-py311h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy >=1.12", - "updated": "numpy >=1.12,<2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "autograd-1.5-py312h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy >=1.12", - "updated": "numpy >=1.12,<2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "autograd-1.5-py39h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy >=1.12", - "updated": "numpy >=1.12,<2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "biopython-1.77-py39h27cfd23_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "biopython-1.78-py310h7f8727e_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "biopython-1.78-py311h5eee18b_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "biopython-1.78-py312h5eee18b_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "biopython-1.78-py39h7f8727e_0.tar.bz2", - "type": "dep", - "original": "numpy", - "updated": "numpy <2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": "bkcharts-0.2-py310h06a4308_0.tar.bz2", - "type": "dep", - "original": "numpy >=1.7.1", - "updated": "numpy >=1.7.1,<2.0a0" - }, - { - "subdirectory": "linux-64", - "filename": 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2024 20:44:45 +0100 Subject: [PATCH 40/47] README updated with changes --- README.md | 37 ++++++------------------------------- 1 file changed, 6 insertions(+), 31 deletions(-) diff --git a/README.md b/README.md index c671963..52fdcc5 100644 --- a/README.md +++ b/README.md @@ -47,17 +47,17 @@ We should put things on the revoke list when: ## Numpy 2.0 Compatibility Checks and Updates -### Running numpy2.py +### Running `generate_numpy2_patch.py` -The `numpy2.py` script is used to check and update package dependencies for compatibility with numpy 2.0. To run the script, use the following command: +The `generate_numpy2_patch.py` script is used to check and update package dependencies for compatibility with numpy 2.0. To run the script, use the following command: ``` -python numpy2.py +python `generate_numpy2_patch.py` ``` ### What numpy2.py does -`numpy2.py` performs the following tasks: +`generate_numpy2_patch.py` performs the following tasks: 1. Scans through the repodata for packages depending on numpy. 2. Checks if these dependencies need updates to ensure compatibility with numpy 2.0. 3. Proposes changes to add upper bounds to numpy dependencies where necessary. @@ -65,14 +65,14 @@ python numpy2.py ### When to use numpy2.py -Use `numpy2.py` when: +Use `generate_numpy2_patch.py` when: - Preparing for a major numpy version update (e.g., transitioning to numpy 2.0). - You need to audit and update numpy dependencies across many packages. - You want to ensure compatibility of the ecosystem with upcoming numpy versions. ### Running main.py with proposed_numpy_changes.json -After running `numpy2.py`, you'll have a `numpy2_patch.json` file. To apply these changes: +After running `generate_numpy2_patch.py`, you'll have a `numpy2_patch.json` file. To apply these changes: 1. Ensure `numpy2_patch.json` is in the same directory as `main.py`. 2. Run `main.py` as usual: @@ -83,31 +83,6 @@ python main.py `main.py` will automatically detect and incorporate the changes from `numpy2_patch.json` into the hotfix process. -## Reviewing CSV Updates - -After running `numpy2.py` or `main.py`, CSV files are generated containing detailed information about the proposed changes. To review these updates: - -1. Locate the generated CSV files in your working directory. They will be named according to the type of update, e.g., `dep_numpy2_updates.csv`, `constr_numpy2_updates.csv`. - -2. For a quick review, you can open these files with any spreadsheet application on your local machine. - -3. For a more collaborative review or to share the updates with your team, you can upload the CSV files to a cloud-based service: - - - Google Sheets: - 1. Go to [Google Sheets](https://sheets.google.com). - 2. Click on "Blank" to create a new spreadsheet. - 3. Go to File > Import > Upload and select your CSV file. - 4. Choose your import options and click "Import data". - -4. Once uploaded, you can easily sort, filter, and analyze the proposed changes. Look for: - - Packages affected - - Types of changes (e.g., adding upper bounds, modifying existing bounds) - - Reasons for changes - -5. Use this review to make informed decisions about which changes to approve or modify before applying the hotfixes. - -Remember to handle these CSVs securely, especially if they contain sensitive package information. - ## Utility scripts: ### Seeing current hotfixes with `gen-current-hotfix-report.py`: From e5bb64f30237de0c3decb784c1c89dacc99c4067 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 8 Aug 2024 10:42:18 +0100 Subject: [PATCH 41/47] make changes for legibility to per review --- generate_numpy2_patch.py | 107 ++++++++++++++++++++++++++------------- main.py | 11 ++-- 2 files changed, 79 insertions(+), 39 deletions(-) diff --git a/generate_numpy2_patch.py b/generate_numpy2_patch.py index 3852ca2..0feac97 100644 --- a/generate_numpy2_patch.py +++ b/generate_numpy2_patch.py @@ -128,53 +128,81 @@ def update_numpy_dependencies(dependencies_list, package_record, dependency_type - package_subdir: Package location subdirectory. - filename: Package filename. """ - add_bound_to_unspecified = True + # Flag to determine if unspecified dependencies should get an upper bound + add_bound_to_unspecified = True + + # Iterate through each dependency in the list for _, dependency in enumerate(dependencies_list): parts = dependency.split() package_name = parts[0] - if package_name in ["numpy", "numpy-base"]: - if not has_upper_bound(dependency): - if package_name in numpy2_protect_dict: - version_str = parts[1] if len(parts) > 1 else None - version = parse_version(version_str) if version_str else None - protected_version = parse_version(numpy2_protect_dict[package_name]) - if version and protected_version: - try: - if VersionOrder(version) <= VersionOrder(protected_version): - new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" - collect_proposed_change(package_subdir, filename, dependency_type, dependency, - new_dependency, "Version <= protected_version") - except ValueError: - new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" - collect_proposed_change(package_subdir, filename, dependency_type, dependency, - new_dependency, "Version comparison failed") - elif add_bound_to_unspecified: - if len(parts) > 1: - new_dependency = patch_record_with_fixed_deps(dependency, parts) - if new_dependency != dependency: - collect_proposed_change(package_subdir, filename, dependency_type, dependency, - new_dependency, "Upper bound added") - else: - new_dependency = f"{dependency} <2.0a0" - collect_proposed_change(package_subdir, filename, dependency_type, dependency, - new_dependency, "Upper bound added") + + # Check if the dependency is for numpy and does not have an upper bound + if "numpy" in package_name and not has_upper_bound(dependency): + if package_name in numpy2_protect_dict: + # Handle dependencies that are in the protection dictionary + _handle_protected_dependency(parts, dependency, package_subdir, filename, dependency_type) + elif add_bound_to_unspecified: + # Handle dependencies that are unspecified and need an upper bound + _handle_unspecified_dependency(parts, dependency, package_subdir, filename, dependency_type) + + +def _handle_protected_dependency(parts, dependency, package_subdir, filename, dependency_type): + """ + Handles dependencies that are in the protection dictionary. + """ + version_str = parts[1] if len(parts) > 1 else None + version = parse_version(version_str) if version_str else None + protected_version = parse_version(numpy2_protect_dict[parts[0]]) + + if version and protected_version: + try: + # Compare the version with the protected version + if VersionOrder(version) <= VersionOrder(protected_version): + # Add an upper bound to the dependency if the version is less than or equal to the protected version + new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" + collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Version <= protected_version") + except ValueError: + # Handle version comparison errors + new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" + collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Version comparison failed") + + +def _handle_unspecified_dependency(parts, dependency, package_subdir, filename, dependency_type): + """ + Handles dependencies that are unspecified and need an upper bound. + """ + if len(parts) > 1: + # Patch the record with fixed dependencies if there are multiple parts + new_dependency = patch_record_with_fixed_deps(dependency, parts) + if new_dependency != dependency: + collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Upper bound added") + else: + # Add an upper bound to the dependency if there is only one part + new_dependency = f"{dependency} <2.0a0" + collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Upper bound added") def main(): - base_dir = Path(__file__).parent / CHANNEL_NAME + base_dir = Path(__file__).parent / CHANNEL_NAME repodatas = {} + + # Iterate over each subdir to load or fetch repodata for subdir in SUBDIRS: repodata_path = base_dir / subdir / "repodata_from_packages.json" + + # Check if the repodata file exists locally if repodata_path.is_file(): with repodata_path.open() as fh: - repodatas[subdir] = json.load(fh) + repodatas[subdir] = json.load(fh) # Load repodata from local file else: + # Fetch repodata from the remote URL if not available locally repodata_url = f"{CHANNEL_ALIAS}/{CHANNEL_NAME}/{subdir}/repodata_from_packages.json" response = requests.get(repodata_url) response.raise_for_status() - repodatas[subdir] = response.json() - repodata_path.parent.mkdir(parents=True, exist_ok=True) + repodatas[subdir] = response.json() # Load repodata from the response + repodata_path.parent.mkdir(parents=True, exist_ok=True) # Ensure the directory exists with repodata_path.open('w') as fh: + # Save the fetched repodata to a local file json.dump( repodatas[subdir], fh, @@ -182,6 +210,8 @@ def main(): sort_keys=True, separators=(",", ": "), ) + + # Process each subdir's repodata to update numpy dependencies for subdir in SUBDIRS: index = repodatas[subdir]["packages"] for fn, record in index.items(): @@ -189,22 +219,29 @@ def main(): depends = record["depends"] constrains = record.get("constrains", []) + # Filter out None dependencies depends = [dep for dep in depends if dep is not None] + + # Check if the package is for specific Python versions if any(py_ver in fn for py_ver in ["py39", "py310", "py311", "py312"]): + # Exclude certain package names from processing if name not in ["anaconda", "_anaconda_depends", "__anaconda_core_depends", "_anaconda_core"]: try: + # Update numpy dependencies in the 'depends' list for dep in depends: if dep.split()[0] in ["numpy", "numpy-base"]: - update_numpy_dependencies(depends, record, "dep", subdir, fn) + update_numpy_dependencies(depends, record, "depends", subdir, fn) + # Update numpy dependencies in the 'constrains' list for constrain in constrains: if constrain.split()[0] in ["numpy", "numpy-base"]: - update_numpy_dependencies(constrains, record, "constr", subdir, fn) + update_numpy_dependencies(constrains, record, "constrains", subdir, fn) except Exception as e: + # Log any errors encountered during the update process logger.error(f"numpy 2.0.0 error {fn}: {e}") + # Write the proposed changes to a JSON file json_filename = Path("numpy2_patch.json") - with json_filename.open('w') as f: - json.dump(dict(NUMPY_2_CHANGES), f, indent=2) + json_filename.write_text(json.dumps(dict(NUMPY_2_CHANGES), indent=2)) logger.info(f"Proposed changes have been written to {json_filename}") diff --git a/main.py b/main.py index 8485fa3..221c29e 100644 --- a/main.py +++ b/main.py @@ -291,10 +291,8 @@ def apply_numpy2_changes(record, subdir, filename): if not change: return else: - try: - replace_dep(record[change["type"]], change["original"], change["updated"]) - except KeyError: - pass + replace_dep(record[change["type"]], change["original"], change["updated"]) + def _replace_vc_features_with_vc_pkg_deps(name, record, depends): @@ -1471,6 +1469,11 @@ def patch_record_in_place(fn, record, subdir): ########### # Numpy 2.0.0 Patch + + # Numpy 2.0.0 hotfix will allow a bulk of packages to be locked to below 2.0.0 as the interoperability + # between numpy 1.x and 2.x is not guaranteed. + + # This will ensure upper bounds on numpy for all packages that are not confirmed to be compatible with numpy 2.0.0 if NUMPY_2_CHANGES: apply_numpy2_changes(record, subdir, fn) From 3b6625c54cdb3297a715e2113ea63d69f3821d47 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Thu, 8 Aug 2024 10:46:02 +0100 Subject: [PATCH 42/47] linting correctors --- generate_numpy2_patch.py | 24 ++++++++++++++---------- main.py | 1 - 2 files changed, 14 insertions(+), 11 deletions(-) diff --git a/generate_numpy2_patch.py b/generate_numpy2_patch.py index 0feac97..e0b5069 100644 --- a/generate_numpy2_patch.py +++ b/generate_numpy2_patch.py @@ -129,7 +129,7 @@ def update_numpy_dependencies(dependencies_list, package_record, dependency_type - filename: Package filename. """ # Flag to determine if unspecified dependencies should get an upper bound - add_bound_to_unspecified = True + add_bound_to_unspecified = True # Iterate through each dependency in the list for _, dependency in enumerate(dependencies_list): @@ -150,8 +150,8 @@ def _handle_protected_dependency(parts, dependency, package_subdir, filename, de """ Handles dependencies that are in the protection dictionary. """ - version_str = parts[1] if len(parts) > 1 else None - version = parse_version(version_str) if version_str else None + version_str = parts[1] if len(parts) > 1 else None + version = parse_version(version_str) if version_str else None protected_version = parse_version(numpy2_protect_dict[parts[0]]) if version and protected_version: @@ -160,11 +160,13 @@ def _handle_protected_dependency(parts, dependency, package_subdir, filename, de if VersionOrder(version) <= VersionOrder(protected_version): # Add an upper bound to the dependency if the version is less than or equal to the protected version new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" - collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Version <= protected_version") + collect_proposed_change(package_subdir, filename, dependency_type, + dependency, new_dependency, "Version <= protected_version") except ValueError: # Handle version comparison errors new_dependency = f"{dependency},<2.0a0" if len(parts) > 1 else f"{dependency} <2.0a0" - collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Version comparison failed") + collect_proposed_change(package_subdir, filename, dependency_type, + dependency, new_dependency, "Version comparison failed") def _handle_unspecified_dependency(parts, dependency, package_subdir, filename, dependency_type): @@ -175,21 +177,23 @@ def _handle_unspecified_dependency(parts, dependency, package_subdir, filename, # Patch the record with fixed dependencies if there are multiple parts new_dependency = patch_record_with_fixed_deps(dependency, parts) if new_dependency != dependency: - collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Upper bound added") + collect_proposed_change(package_subdir, filename, dependency_type, + dependency, new_dependency, "Upper bound added") else: # Add an upper bound to the dependency if there is only one part new_dependency = f"{dependency} <2.0a0" - collect_proposed_change(package_subdir, filename, dependency_type, dependency, new_dependency, "Upper bound added") + collect_proposed_change(package_subdir, filename, dependency_type, + dependency, new_dependency, "Upper bound added") def main(): - base_dir = Path(__file__).parent / CHANNEL_NAME + base_dir = Path(__file__).parent / CHANNEL_NAME repodatas = {} # Iterate over each subdir to load or fetch repodata for subdir in SUBDIRS: repodata_path = base_dir / subdir / "repodata_from_packages.json" - + # Check if the repodata file exists locally if repodata_path.is_file(): with repodata_path.open() as fh: @@ -221,7 +225,7 @@ def main(): # Filter out None dependencies depends = [dep for dep in depends if dep is not None] - + # Check if the package is for specific Python versions if any(py_ver in fn for py_ver in ["py39", "py310", "py311", "py312"]): # Exclude certain package names from processing diff --git a/main.py b/main.py index 221c29e..085b33a 100644 --- a/main.py +++ b/main.py @@ -294,7 +294,6 @@ def apply_numpy2_changes(record, subdir, filename): replace_dep(record[change["type"]], change["original"], change["updated"]) - def _replace_vc_features_with_vc_pkg_deps(name, record, depends): python_vc_deps = { "2.6": "vc 9.*", From c54945f44ff3e2d9042f3136b7df2ccee9b68c8e Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 13 Aug 2024 11:39:31 +0100 Subject: [PATCH 43/47] remove correction code --- generate_numpy2_patch.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/generate_numpy2_patch.py b/generate_numpy2_patch.py index e0b5069..5ee916f 100644 --- a/generate_numpy2_patch.py +++ b/generate_numpy2_patch.py @@ -51,12 +51,6 @@ def collect_proposed_change(subdirectory, filename, change_type, original_depend - updated_dependency: The updated dependency string. - reason: The reason for the change. """ - # change dep and constr to dependency and constraint - if change_type == "dep": - change_type = "depends" - elif change_type == "constr": - change_type = "constrains" - NUMPY_2_CHANGES[subdirectory][filename] = { "type": change_type, "original": original_dependency, From 36222d0f551d3da68417960efaa564718d79d6ed Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 13 Aug 2024 11:41:20 +0100 Subject: [PATCH 44/47] revert to force git to pick up the change --- generate_numpy2_patch.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/generate_numpy2_patch.py b/generate_numpy2_patch.py index 5ee916f..091fa01 100644 --- a/generate_numpy2_patch.py +++ b/generate_numpy2_patch.py @@ -228,11 +228,11 @@ def main(): # Update numpy dependencies in the 'depends' list for dep in depends: if dep.split()[0] in ["numpy", "numpy-base"]: - update_numpy_dependencies(depends, record, "depends", subdir, fn) + update_numpy_dependencies(depends, record, "dep", subdir, fn) # Update numpy dependencies in the 'constrains' list for constrain in constrains: if constrain.split()[0] in ["numpy", "numpy-base"]: - update_numpy_dependencies(constrains, record, "constrains", subdir, fn) + update_numpy_dependencies(constrains, record, "const", subdir, fn) except Exception as e: # Log any errors encountered during the update process logger.error(f"numpy 2.0.0 error {fn}: {e}") From 4d8e248759967558ffa234f11bd39500440338b3 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 13 Aug 2024 11:41:39 +0100 Subject: [PATCH 45/47] revert depends and contrains --- generate_numpy2_patch.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/generate_numpy2_patch.py b/generate_numpy2_patch.py index 091fa01..5ee916f 100644 --- a/generate_numpy2_patch.py +++ b/generate_numpy2_patch.py @@ -228,11 +228,11 @@ def main(): # Update numpy dependencies in the 'depends' list for dep in depends: if dep.split()[0] in ["numpy", "numpy-base"]: - update_numpy_dependencies(depends, record, "dep", subdir, fn) + update_numpy_dependencies(depends, record, "depends", subdir, fn) # Update numpy dependencies in the 'constrains' list for constrain in constrains: if constrain.split()[0] in ["numpy", "numpy-base"]: - update_numpy_dependencies(constrains, record, "const", subdir, fn) + update_numpy_dependencies(constrains, record, "constrains", subdir, fn) except Exception as e: # Log any errors encountered during the update process logger.error(f"numpy 2.0.0 error {fn}: {e}") From b6595afd04a669fe92c41ebd3b5faae29d372ffc Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 13 Aug 2024 11:43:32 +0100 Subject: [PATCH 46/47] ensure return case is not needed --- main.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/main.py b/main.py index 085b33a..bb14efa 100644 --- a/main.py +++ b/main.py @@ -288,9 +288,7 @@ def apply_numpy2_changes(record, subdir, filename): return change = NUMPY_2_CHANGES[subdir].get(filename) - if not change: - return - else: + if change: replace_dep(record[change["type"]], change["original"], change["updated"]) From 4d468b180543211231e77ac074507091fb7a1f92 Mon Sep 17 00:00:00 2001 From: Jamie Robertson Date: Tue, 13 Aug 2024 13:33:14 +0100 Subject: [PATCH 47/47] remove protect dict to await issues --- generate_numpy2_patch.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/generate_numpy2_patch.py b/generate_numpy2_patch.py index 5ee916f..56e78ca 100644 --- a/generate_numpy2_patch.py +++ b/generate_numpy2_patch.py @@ -7,10 +7,8 @@ from conda.models.version import VersionOrder numpy2_protect_dict = { - 'pandas': '2.2.2', - 'scikit-learn': '1.4.2', - 'pyamg': '4.2.3', - 'pyqtgraph': '0.13.1' + # add any numpy dependencies that needs to be protected here + # "package_name": "protected_version" } proposed_changes = []