Merge pull request #2 from scverse-bot/template-update-zunderlab-esch…

…r-v0.3.1

Update template to v0.3.1

.codecov.yaml

@@ -1,17 +1,17 @@
 # Based on pydata/xarray
 codecov:
-    require_ci_to_pass: no
+  require_ci_to_pass: no
 
 coverage:
-    status:
-        project:
-            default:
-                # Require 1% coverage, i.e., always succeed
-                target: 1
-        patch: false
-        changes: false
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
 
 comment:
-    layout: diff, flags, files
-    behavior: once
-    require_base: no
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

.cruft.json

@@ -1,23 +1,29 @@
 {
-    "template": "https://github.com/scverse/cookiecutter-scverse",
-    "commit": "7b86b3572123c7777e012adcf6fff0c7217ba7a0",
-    "checkout": null,
-    "context": {
-        "cookiecutter": {
-            "project_name": "eschr",
-            "package_name": "eschr",
-            "project_description": "A hyperparameter-randomized ensemble approach for robust clustering across diverse datasets",
-            "author_full_name": "Sarah Goggin",
-            "author_email": "[email protected]",
-            "github_user": "zunderlab",
-            "project_repo": "https://github.com/zunderlab/eschr",
-            "license": "MIT License",
-            "_copy_without_render": [
-                ".github/workflows/**.yaml",
-                "docs/_templates/autosummary/**.rst"
-            ],
-            "_template": "https://github.com/scverse/cookiecutter-scverse"
-        }
-    },
-    "directory": null
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "586b1652162ff7994b0070a034023d64289ae416",
+  "checkout": "v0.3.1",
+  "context": {
+    "cookiecutter": {
+      "project_name": "eschr",
+      "package_name": "eschr",
+      "project_description": "A hyperparameter-randomized ensemble approach for robust clustering across diverse datasets",
+      "author_full_name": "Sarah Goggin",
+      "author_email": "[email protected]",
+      "github_user": "zunderlab",
+      "project_repo": "https://github.com/zunderlab/eschr",
+      "license": "MIT License",
+      "_copy_without_render": [
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse"
+    }
+  },
+  "directory": null
 }

.editorconfig

@@ -8,5 +8,11 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
+[*.{yml,yaml}]
+indent_size = 2
+
+[.cruft.json]
+indent_size = 2
+
 [Makefile]
 indent_style = tab

.gitignore

@@ -1,9 +1,13 @@
 # Temp files
 .DS_Store
 *~
+buck-out/
 
 # Compiled files
+.venv/
 __pycache__/
+.mypy_cache/
+.ruff_cache/
 
 # Distribution / packaging
 /build/

.pre-commit-config.yaml.rej

@@ -0,0 +1,124 @@
+diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml	(rejected hunks)
+@@ -1,85 +1,42 @@
+ fail_fast: false
+ default_language_version:
+-    python: python3
++  python: python3
+ default_stages:
+-    - commit
+-    - push
++  - commit
++  - push
+ minimum_pre_commit_version: 2.16.0
+ repos:
+-    - repo: https://github.com/psf/black
+-      rev: 24.2.0
+-      hooks:
+-          - id: black
+-    - repo: https://github.com/pre-commit/mirrors-prettier
+-      rev: v4.0.0-alpha.8
+-      hooks:
+-          - id: prettier
+-            # Newer versions of node don't work on systems that have an older version of GLIBC
+-            # (in particular Ubuntu 18.04 and Centos 7)
+-            # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+-            # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+-            # https://github.com/jupyterlab/jupyterlab/issues/12675
+-            language_version: "17.9.1"
+-    - repo: https://github.com/asottile/blacken-docs
+-      rev: 1.16.0
+-      hooks:
+-          - id: blacken-docs
+-    - repo: https://github.com/PyCQA/isort
+-      rev: 5.13.2
+-      hooks:
+-          - id: isort
+-    - repo: https://github.com/asottile/yesqa
+-      rev: v1.5.0
+-      hooks:
+-          - id: yesqa
+-            additional_dependencies:
+-                - flake8-tidy-imports
+-                - flake8-docstrings
+-                - flake8-rst-docstrings
+-                - flake8-comprehensions
+-                - flake8-bugbear
+-                - flake8-blind-except
+-    - repo: https://github.com/pre-commit/pre-commit-hooks
+-      rev: v4.5.0
+-      hooks:
+-          - id: detect-private-key
+-          - id: check-ast
+-          - id: end-of-file-fixer
+-          - id: mixed-line-ending
+-            args: [--fix=lf]
+-          - id: trailing-whitespace
+-          - id: check-case-conflict
+-    - repo: https://github.com/myint/autoflake
+-      rev: v2.3.0
+-      hooks:
+-          - id: autoflake
+-            args:
+-                - --in-place
+-                - --remove-all-unused-imports
+-                - --remove-unused-variable
+-                - --ignore-init-module-imports
+-    - repo: https://github.com/PyCQA/flake8
+-      rev: 7.0.0
+-      hooks:
+-          - id: flake8
+-            additional_dependencies:
+-                - flake8-tidy-imports
+-                - flake8-docstrings
+-                - flake8-rst-docstrings
+-                - flake8-comprehensions
+-                - flake8-bugbear
+-                - flake8-blind-except
+-    - repo: https://github.com/asottile/pyupgrade
+-      rev: v3.15.1
+-      hooks:
+-          - id: pyupgrade
+-            args: [--py3-plus, --py38-plus, --keep-runtime-typing]
+-    - repo: local
+-      hooks:
+-          - id: forbid-to-commit
+-            name: Don't commit rej files
+-            entry: |
+-                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+-                Fix the merge conflicts manually and remove the .rej files.
+-            language: fail
+-            files: '.*\.rej$'
++  - repo: https://github.com/pre-commit/mirrors-prettier
++    rev: v4.0.0-alpha.8
++    hooks:
++      - id: prettier
++  - repo: https://github.com/astral-sh/ruff-pre-commit
++    rev: v0.2.2
++    hooks:
++      - id: ruff
++        types_or: [python, pyi, jupyter]
++        args: [--fix, --exit-non-zero-on-fix]
++      - id: ruff-format
++        types_or: [python, pyi, jupyter]
++  - repo: https://github.com/pre-commit/pre-commit-hooks
++    rev: v4.5.0
++    hooks:
++      - id: detect-private-key
++      - id: check-ast
++      - id: end-of-file-fixer
++      - id: mixed-line-ending
++        args: [--fix=lf]
++      - id: trailing-whitespace
++      - id: check-case-conflict
++      # Check that there are no merge conflicts (could be generated by template sync)
++      - id: check-merge-conflict
++        args: [--assume-in-merge]
++  - repo: local
++    hooks:
++      - id: forbid-to-commit
++        name: Don't commit rej files
++        entry: |
++          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
++          Fix the merge conflicts manually and remove the .rej files.
++        language: fail
++        files: '.*\.rej$'

.readthedocs.yaml.rej

@@ -0,0 +1,29 @@
+diff a/.readthedocs.yaml b/.readthedocs.yaml	(rejected hunks)
+@@ -1,16 +1,16 @@
+ # https://docs.readthedocs.io/en/stable/config-file/v2.html
+ version: 2
+ build:
+-    os: ubuntu-20.04
+-    tools:
+-        python: "3.10"
++  os: ubuntu-20.04
++  tools:
++    python: "3.10"
+ sphinx:
+-    configuration: docs/conf.py
+-    # disable this for more lenient docs builds
+-    fail_on_warning: true
++  configuration: docs/conf.py
++  # disable this for more lenient docs builds
++  fail_on_warning: true
+ python:
+-    install:
+-        - method: pip
+-          path: .
+-          extra_requirements:
+-              - doc
++  install:
++    - method: pip
++      path: .
++      extra_requirements:
++        - doc

README.md.rej

@@ -0,0 +1,10 @@
+diff a/README.md b/README.md	(rejected hunks)
+@@ -17,7 +17,7 @@ Please refer to the [documentation][link-docs]. In particular, the
+
+ ## Installation
+
+-You need to have Python 3.8 or newer installed on your system. If you don't have
++You need to have Python 3.9 or newer installed on your system. If you don't have
+ Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+
+ There are several alternative options to install eschr:

docs/_static/css/custom.css

@@ -0,0 +1,4 @@
+/* Reduce the font size in data frames - See https://github.com/scverse/cookiecutter-scverse/issues/193 */
+div.cell_output table.dataframe {
+    font-size: 0.8em;
+}

docs/_templates/autosummary/class.rst

@@ -39,9 +39,6 @@ Attributes
 
 {% for item in attributes %}
 
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
 .. autoattribute:: {{ [objname, item] | join(".") }}
 {%- endfor %}
 
@@ -56,9 +53,6 @@ Methods
 {% for item in methods %}
 {%- if item != '__init__' %}
 
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
 .. automethod:: {{ [objname, item] | join(".") }}
 {%- endif -%}
 {%- endfor %}