fix: dependecies and conda build by GregaVrbancic · Pull Request #720 · NiaOrg/NiaPy

GregaVrbancic · 2025-11-21T11:26:42Z

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GregaVrbancic · 2025-11-21T11:49:24Z

@firefly-cpp, in order to enable the numpy >2, we have to drop the support for Python version <3.10

Copilot

Pull Request Overview

This PR updates Python version support and dependency versions across the project, modernizes the conda build configuration, and adds new CI/CD workflows for testing conda builds. The PR drops Python 3.9 support in favor of Python 3.10-3.13.

Key changes:

Updates minimum Python version from 3.9 to 3.10 and adds support for Python 3.13
Upgrades core dependencies (numpy, pandas, matplotlib, etc.) to newer major/minor versions
Modernizes conda build configuration with noarch builds and explicit dependency management

Reviewed Changes

Copilot reviewed 8 out of 9 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
pyproject.toml	Adds Python 3.10-3.13 classifiers, updates Python requirement to >=3.10, upgrades all dependency versions
conda/meta.yaml	Adds noarch build configuration, explicit runtime dependencies, and poetry-core to build requirements
conda/conda_build_config.yaml	Updates Python versions list from 3.9-3.12 to 3.10-3.13
.pyup.yml	New configuration file for PyUp dependency updates with monthly schedule and dependency filtering
.github/workflows/test_conda.yml	New workflow for testing conda builds on pull requests
.github/workflows/publish_conda.yml	Modernizes conda publishing workflow with updated actions and manual build/upload steps
.github/workflows/main.yml	Updates test matrix to Python 3.10-3.13 and upgrades macOS runner to macos-14
.github/dependabot.yml	Replaces separate pip directory config with ignore rules for optional dependencies

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Copilot · 2025-11-21T11:53:47Z

@GregaVrbancic I've opened a new pull request, #721, to work on those changes. Once the pull request is ready, I'll request review from you.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Initial plan * fix: align Python version requirement in conda/meta.yaml with pyproject.toml Co-authored-by: GregaVrbancic <1894788+GregaVrbancic@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: GregaVrbancic <1894788+GregaVrbancic@users.noreply.github.com> Co-authored-by: Grega Vrbančič <grega.vrbancic@gmail.com>

Copilot

Pull Request Overview

Copilot reviewed 8 out of 9 changed files in this pull request and generated 5 comments.

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Copilot · 2025-11-21T12:02:40Z

-openpyxl = "^3.1.2"
-matplotlib = "^3.8.0"
+python = ">=3.10,<3.14"
+numpy = "^2.1.1"


The update from numpy ^1.26.1 to ^2.1.1 is a major version bump. NumPy 2.0 introduced several breaking changes. Please ensure that the codebase is compatible with NumPy 2.x, as this could affect array behavior, data types, and deprecated APIs. Consider testing thoroughly or documenting this as a breaking change.

Copilot · 2025-11-21T12:02:41Z

 build:
  number: 0
-  script: {{ PYTHON }} -m pip install . -vv
+  noarch: python


The conda build configuration now uses noarch: python to create a platform-independent package. However, some dependencies (numpy, pandas, matplotlib) have native extensions that are platform-specific. Verify that these dependencies correctly provide noarch builds or that the conda build will properly handle platform-specific dependencies at install time.

Suggested change

noarch: python

Copilot · 2025-11-21T12:02:41Z

+
+# Only update direct dependencies in pyproject.toml main group
+# Ignore all optional dependencies and transitive dependencies
+update: insecure


[nitpick] The update: insecure setting will only update packages with known security vulnerabilities. Combined with the extensive ignore list, this means most dependency updates will be missed. Consider using update: all or update: security if you want to receive updates for important bug fixes and improvements, not just security patches.

Suggested change

update: insecure

update: all

Copilot · 2025-11-21T12:02:41Z

+      run: |
+        conda install -y conda-build anaconda-client
+        conda build conda --output-folder build
+        anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload build/noarch/*.conda --force


[nitpick] The --force flag in the anaconda upload command will overwrite existing packages without prompting. While this may be intentional for automated releases, consider whether this could accidentally overwrite a published package. If this is the desired behavior for re-publishing, it's fine; otherwise, consider removing --force to prevent accidental overwrites.

Suggested change

anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload build/noarch/*.conda --force

anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload build/noarch/*.conda

Copilot · 2025-11-21T12:02:42Z

 python:
-  - 3.9
  - 3.10
  - 3.11
-  - 3.12
+  - 3.12
+  - 3.13


Since meta.yaml now specifies noarch: python, the conda package will be built as platform-independent. However, this file still defines multiple Python versions (3.10-3.13). With noarch: python, conda-build typically ignores the Python version matrix and creates a single package compatible with all specified Python versions. Consider removing this file or adding a comment explaining that these versions define the compatibility range rather than build matrix.

firefly-cpp

Perfect. Please proceed with the new release of this package. The Python versions appear to meet the requirements for most platforms.

GregaVrbancic added 7 commits November 21, 2025 12:26

fix: dependecies and conda build

22318fb

fix: add setuptools and wheel to conda build requirements

40b1887

ci: use short CONDA_BLD_PATH and CONDA_PKGS_DIRS to avoid long path e…

a57180e

…rrors

fix: add missing files

f5edc2c

fix: use inline script instead of build.sh file to avoid conda-build …

3eb357a

…conflict

fix: remove outdated conda-verify step (doesn't support Python 3.13)

6d5c342

fix: update workflows to use modern .conda package format instead of …

3494e8d

….tar.bz2

GregaVrbancic requested review from Copilot and firefly-cpp November 21, 2025 11:50

Copilot started reviewing on behalf of GregaVrbancic November 21, 2025 11:50 View session

Copilot finished reviewing on behalf of GregaVrbancic November 21, 2025 11:51

Copilot AI reviewed Nov 21, 2025

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Comment thread pyproject.toml Outdated

Comment thread conda/meta.yaml Outdated

Comment thread conda/meta.yaml Outdated

Comment thread conda/meta.yaml Outdated

Copilot AI mentioned this pull request Nov 21, 2025

Align Python version requirements between pip and conda #721

Merged

GregaVrbancic and others added 3 commits November 21, 2025 12:54

Update conda/meta.yaml

3ca5ebe

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update pyproject.toml

b41176d

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

GregaVrbancic requested a review from Copilot November 21, 2025 11:59

Copilot started reviewing on behalf of GregaVrbancic November 21, 2025 11:59 View session

Copilot finished reviewing on behalf of GregaVrbancic November 21, 2025 12:01

Copilot AI reviewed Nov 21, 2025

View reviewed changes

firefly-cpp approved these changes Nov 21, 2025

View reviewed changes

GregaVrbancic merged commit 2f86304 into master Nov 21, 2025
22 checks passed

firefly-cpp mentioned this pull request Nov 21, 2025

Numpy version causes conflicts with other packages that use numpy > 2.x.x #719

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fix: dependecies and conda build#720

fix: dependecies and conda build#720
GregaVrbancic merged 10 commits intomasterfrom
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	anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload build/noarch/*.conda --force
	anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload build/noarch/*.conda

               python:
-                - 3.9
                 - 3.10
                 - 3.11
-                - 3.12

                
                    No newline at end of file
+                - 3.12
+                - 3.13

                
                    No newline at end of file

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