feat: Update dependencies to latest versions - less complex #1011

bgruening · 2024-10-18T15:51:29Z

No description provided.

coderabbitai · 2024-10-18T15:55:31Z

Walkthrough

The changes in the pull request focus on updating the bioconda_utils-requirements.txt file, specifically involving version modifications for several dependencies. The conda and conda-build versions have been increased from 24.5.* to 24.9.* and from 24.5.* to 24.7.*, respectively. The conda-index version has been raised from 0.4.* to 0.5.*, and the conda-package-streaming version has been updated from 0.9.* to 0.11.*. Additionally, the boa dependency has been commented out, indicating it is no longer necessary.

Other dependencies, including argh, colorlog, tqdm, yaspin, ruamel.yaml, pyaml, networkx, pandas, libblas, boltons, jsonschema, and jinja2, have not been altered. The anaconda-client, galaxy-tool-util, involucro, skopeo, findutils, and git dependencies also remain unchanged. The regex dependency has been specified with a version of 2024.*, while the backoff library is now set to 2.2.*. Other dependencies like gitpython, gidgethub, and pyjwt have not changed, with pyjwt requiring a minimum version of 2.4.0. The dependencies beautifulsoup4, requests, pygithub, diskcache, platformdirs, and tabulate remain unchanged.

Additionally, the versioneer.py file has undergone several modifications. The SafeConfigParser has been replaced with ConfigParser, affecting how configuration files are read. The error handling in the get_config_from_root function has been improved for clarity. The logic for retrieving version information has been streamlined, and the run_command function has been modified for better command execution and error reporting. Comments and documentation within the code have also been updated for clarity. The test/test_utils.py file has seen changes to import statements and exception handling to enhance error reporting during tests.

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coderabbitai

Actionable comments posted: 1

📜 Review details

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Review profile: CHILL

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Files that changed from the base of the PR and between a4560e5 and f3d1805.

📒 Files selected for processing (1)

versioneer.py (1 hunks)

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versioneer.py

aliciaaevans · 2024-10-18T18:54:48Z

FAILED test/test_utils.py::test_rendering_sandboxing - conda_build.exceptions.CondaBuildUserError: Failed to render jinja template in /var/folders/4b/7k50gk0j4f5bjk3799wdt8nw0000gn/T/tmptggrcmcr/one/meta.yaml:
'GITHUB_TOKEN' is undefined

I think this is the cause: conda/conda-build#5371

coderabbitai

Actionable comments posted: 1

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Files that changed from the base of the PR and between aa0dc8d and 0ef7da9.

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test/test_utils.py (2 hunks)

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🪛 Ruff

test/test_utils.py

17-17: conda_build.api imported but unused

Remove unused import: conda_build.api

(F401)

🔇 Additional comments (1)

test/test_utils.py (1)

655-656: Improved exception handling

The change from SystemExit to exceptions.CondaBuildUserError is a good improvement. This modification provides more specific error handling for conda build processes.

This change offers the following benefits:

It provides a more precise exception type, making it easier to distinguish between different error scenarios.

It aligns with best practices by using a custom exception from the conda_build package, which is likely designed for this specific use case.

It improves the overall error handling and debugging capabilities of the test suite.

test/test_utils.py

aliciaaevans · 2024-10-18T19:02:43Z

test/test_utils.py

@@ -652,7 +652,7 @@ def test_rendering_sandboxing():
        assert ("'GITHUB_TOKEN' is undefined" in str(excinfo.value.stdout))
    else:
        # recipe for "one" should fail because GITHUB_TOKEN is not a jinja var.
-        with pytest.raises(SystemExit) as excinfo:
+        with pytest.raises(exceptions.CondaBuildUserError) as excinfo:


Hmm, we might need to update line 644 as well, if that behavior also changed.

bgruening · 2024-10-21T16:34:42Z

🙏

🤖 I have created a release \*beep\* \*boop\* --- ## [3.4.0](https://www.github.com/bioconda/bioconda-utils/compare/v3.3.2...v3.4.0) (2024-10-21) ### Features * Update dependencies to latest versions - less complex ([#1011](https://www.github.com/bioconda/bioconda-utils/issues/1011)) ([167f348](https://www.github.com/bioconda/bioconda-utils/commit/167f348724e77384859e54c23b5226f2e67a1975)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

updates

a4560e5

bgruening closed this Oct 18, 2024

patch versioneer

f3d1805

bgruening reopened this Oct 18, 2024

coderabbitai bot reviewed Oct 18, 2024

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versioneer.py Show resolved Hide resolved

Update bioconda_utils-requirements.txt

aa0dc8d

missing jinja var now throws CondaBuildUserError

0ef7da9

coderabbitai bot reviewed Oct 18, 2024

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aliciaaevans reviewed Oct 18, 2024

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aliciaaevans approved these changes Oct 21, 2024

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bgruening merged commit 167f348 into master Oct 21, 2024
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bgruening deleted the update_deps_2024-10_less branch October 21, 2024 16:34

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feat: Update dependencies to latest versions - less complex #1011

feat: Update dependencies to latest versions - less complex #1011

bgruening commented Oct 18, 2024

coderabbitai bot commented Oct 18, 2024 •

edited

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bgruening commented Oct 21, 2024

feat: Update dependencies to latest versions - less complex #1011

feat: Update dependencies to latest versions - less complex #1011

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bgruening commented Oct 18, 2024

coderabbitai bot commented Oct 18, 2024 • edited Loading

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aliciaaevans commented Oct 18, 2024

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bgruening commented Oct 21, 2024

coderabbitai bot commented Oct 18, 2024 •

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