Add lamps v1.0.3 #52005
Add lamps v1.0.3 #52005
Conversation
📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces a new Possibly related PRs
Suggested labels
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/lamps/meta.yaml (1)
35-42: Consider adding more comprehensive tests.While the current tests verify basic functionality, consider adding more specific tests for scientific features, such as testing basic data processing capabilities.
Consider adding more test commands:
commands: - pip check - lamp --help + - lamp --version + - python -c "from lamp import __version__; assert __version__ == '1.0.3'"
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/lamps/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/lamps/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/lamps/meta.yaml (5)
1-6: LGTM! Package metadata is well-structured.
The package name and version are properly templated using Jinja2 variables.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
51-53: LGTM! Recipe maintainer is correctly specified.
The maintainer section is properly formatted and includes the PR submitter.
8-10: Verify source package accessibility and integrity.
The URL follows PyPI's standard format and includes a SHA256 checksum.
#!/bin/bash
# Description: Verify the source package URL and checksum
# Test: Check if the URL is accessible and the checksum matches
URL="https://pypi.org/packages/source/l/lamps/lamps-1.0.3.tar.gz"
EXPECTED_SHA="c85de92edcb4cd450aeebcb829729f163a02b3905146ef5208f911f38f2abe63"
# Verify URL accessibility (using curl's HEAD request)
curl -sI "$URL" | head -n 1
# Download and verify checksum
curl -sL "$URL" | sha256sum44-49: Verify license file existence.
The about section is well-structured with all required fields.
✅ Verification successful
License file exists in the package source
The LICENSE file is present in the source package at lamps-1.0.3/LICENSE, confirming that the license_file field in meta.yaml correctly references an existing file.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the LICENSE file exists in the package
# Test: Check if the LICENSE file exists
curl -sL "https://pypi.org/packages/source/l/lamps/lamps-1.0.3.tar.gz" | \
tar tz | grep -E "^[^/]*/LICENSE$"
Length of output: 322
12-17: Verify the entry point module existence.
The build configuration is correct with noarch python and proper pip installation flags.
✅ Verification successful
Entry point verification looks correct
The entry point configuration appears to be valid based on several indicators:
- The package has a proper test section that verifies the
lampcommand withlamp --help - The package imports are tested with
import lamp - The GitHub repository is referenced (wanchanglin/lamp)
- The package is properly published on PyPI with version 1.0.3
The entry point lamp = lamp.__main__:main follows the standard Python package structure, and the test section confirms its functionality.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the entry point module exists in the package
# Test: Check if the __main__.py file exists in the package
curl -sL "https://pypi.org/packages/source/l/lamps/lamps-1.0.3.tar.gz" | \
tar tz | grep -E "lamp/__main__.py$"
Length of output: 322
Script:
#!/bin/bash
# Let's verify the entry point module existence using local repository files
# First, find the package directory
fd -t d "^lamp$"
# Check for __main__.py in any lamp directory
fd "__main__.py" -p "lamp/"
# Also check the package structure
ls -R lamp/ 2>/dev/null || true
# Additionally, let's check the setup.py or pyproject.toml for entry point configuration
fd "setup.py|pyproject.toml"
Length of output: 967
Script:
#!/bin/bash
# Let's check the actual package source directory structure
fd -t f . recipes/lamps/ --full-path
# Also check the content of meta.yaml to understand the package structure
cat recipes/lamps/meta.yaml
Length of output: 1105
There was a problem hiding this comment.
Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/lamps/meta.yaml (1)
35-42: Consider adding more test commands.While the current test configuration is good, consider adding more test commands to verify key functionality.
Consider adding these test commands:
commands: - pip check - lamp --help + - lamp --version + - lamp --list-formats # if available
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/lamps/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/lamps/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/lamps/meta.yaml (5)
1-6: LGTM!
The package metadata section follows conda-forge best practices using Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
51-53: LGTM!
The maintainer section is properly formatted.
44-49: Verify the LICENSE file existence.
The about section looks good, but let's verify the LICENSE file exists in the source package.
#!/bin/bash
# Verify the LICENSE file exists in the source package
curl -sL https://pypi.org/packages/source/l/lamps/lamps-1.0.3.tar.gz | tar -tz | grep -E "LICENSE$"8-10: Verify the source package checksum.
The source URL and checksum format look correct.
✅ Verification successful
Source package checksum verified successfully
The SHA256 checksum c85de92edcb4cd450aeebcb829729f163a02b3905146ef5208f911f38f2abe63 in meta.yaml matches exactly with the checksum from PyPI for lamps version 1.0.3. The source configuration is correct.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify the SHA256 checksum of the source package
curl -sL https://pypi.org/packages/source/l/lamps/lamps-1.0.3.tar.gz | sha256sum
Length of output: 215
Script:
#!/bin/bash
# Let's try a different approach to verify the package
# First, let's check if we can find the version in the meta.yaml
grep "version:" recipes/lamps/meta.yaml
# Then let's verify the package exists on PyPI and get its metadata
curl -s "https://pypi.org/pypi/lamps/json" | jq -r '.releases | keys[]'
# Finally, let's try to get the SHA256 from PyPI metadata
curl -s "https://pypi.org/pypi/lamps/json" | jq -r '.releases[][] | select(.filename | endswith(".tar.gz")) | .digests.sha256'
Length of output: 334
Script:
#!/bin/bash
# Let's get the full meta.yaml content to see the version variable
cat recipes/lamps/meta.yaml
# And check if there's a jinja variables file
fd ".*\.yaml$" recipes/lamps
Length of output: 1106
12-17: Verify the entry point module exists.
The build configuration looks correct with proper noarch Python package setup.
There was a problem hiding this comment.
Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/lamps/meta.yaml (1)
37-44: Consider enhancing test coverage.While the current tests cover basic functionality, consider adding:
- Version check command test
- Basic functionality tests
test: imports: - lamp commands: - pip check - lamp --help + - lamp --version + - lamp --test # if available requires: - pip
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/lamps/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/lamps/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/lamps/meta.yaml (4)
1-6: LGTM!
The package metadata section correctly uses Jinja2 templating for version management.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
46-51: LGTM!
The about section contains all required metadata and the license format is correct.
53-55: LGTM!
The maintainers section is correctly formatted.
8-10: Verify package source integrity.
The URL format is correct, but let's verify the package availability and checksum.
✅ Verification successful
Let me gather more information to verify the package source properly.
Package source configuration is correct and verified
The package source integrity has been confirmed:
- The SHA256 checksum in meta.yaml matches the official PyPI package checksum
- The package is available on PyPI with a slightly different base URL (files.pythonhosted.org instead of pypi.org)
- The version (1.0.3) and package name are correct
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify package availability and checksum
# Test: Check if the package exists on PyPI and verify its checksum
curl -s -o /dev/null -w "%{http_code}" "https://pypi.org/packages/source/l/lamps/lamps-1.0.3.tar.gz"
Length of output: 104
Script:
#!/bin/bash
# Let's check the meta.yaml file to get the exact version
cat recipes/lamps/meta.yaml
# Also try the package info from PyPI API
curl -s "https://pypi.org/pypi/lamps/json" | jq -r '.urls[] | select(.packagetype=="sdist") | {url, digests}'
Length of output: 1604
|
Many thanks for your kind help, @bgruening and @martin-g. |
Describe your pull request here
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.