Fix conda builds

[eberrigan]

Description

• conda package tests removed from stage on .conda/meta.yml since conda solver is taking too long.
• conda package tests are now a stage in build_manual.yml and build.yml since we are able to use the libmamba conda-solver in the miniconda set-up.
• Now during the build conda package stage for each OS, the BUILD_PATH is saved as a GITHUB_ENV so it can be used in the next stage.
• The BUILD_PATH is used to create an environment with the conda package for each OS.
• SLEAP is imported and the version of SLEAP is printed to confirm the environment is working for each OS.
• The mac environment has changed to ensure python 3.9 is used every time: conda-forge::python >=3.9.0, <3.10.0.
• qudida and alubmentations are now longer needed in the mac build.sh since they are installed using conda-forge.

Types of changes

• Bugfix
• New feature
• Refactor / Code style update (no logical changes)
• Build / CI changes
• Documentation Update
• Other (explain)

Does this address any currently open issues?

• This is following up pull request Fix ubuntu and mac conda builds #1744 where we moved the conda package tests to the CI because importing sleap during the conda build was either taking forever or failing for macs--see pull request Fix CI on macosx-arm64 #1734.
• After moving the tests to build_manual.yaml by creating a conda environment with the built conda packages, it became clear that the mac build was failing for a different reason then taking forever to resolve with a conda solver.
• The mac build was being allowed to use python 3.10 so it was not building correctly due to the packages being in python 3.9 folders.
• This is also following up dependency updates and fixes such as the TensorFlow conda package Update to new TensorFlow conda package #1726 and the pypi build Fix out of bounds albumentations issues and update dependencies #1724.

Outside contributors checklist

• Review the guidelines for contributing to this repository
• Read and sign the CLA and add yourself to the authors list
• Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
• Add tests that prove your fix is effective or that your feature works
• Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

❤️

[coderabbitai]

Walkthrough

The recent updates focus on enhancing build and test workflows using conda and pip. Changes include reorganizing test configurations, updating Python versions, refining installation commands, and improving GitHub Actions workflows for multi-OS testing. Detailed comments address dependency issues for future maintenance.

Changes

Files/Paths	Change Summaries
.conda/meta.yaml, .conda_mac/condarc.yaml	Moved sleap test config to build workflow; removed unused comment.
.conda_mac/build.sh	Removed specific flags from pip install command.
.conda_mac/meta.yaml	Updated Python version requirement, commented out test imports.
.github/workflows/build_manual.yml	Adjusted branch triggers, build and test steps for multiple OS.
requirements.txt	Added detailed comment on imgstore version issue.
.github/workflows/build.yml, .github/workflows/build_ci.yml	Added test steps for various OS; switched to testing with built wheels.

🐰 In the realm of code, a rabbit did decree,
"Our project evolves with each commit, you see.
Python versions aligned, dependencies now clear,
Testing across systems, without any fear.
With workflows refined and errors effaced,
Our codebase thrives, elegantly encased."

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[coderabbitai]

Actionable comments posted: 0

Review Details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 43a4f13 and 5d576ac.

Files selected for processing (6)

• .conda/meta.yaml (1 hunks)
• .conda_mac/build.sh (1 hunks)
• .conda_mac/condarc.yaml (1 hunks)
• .conda_mac/meta.yaml (3 hunks)
• .github/workflows/build_manual.yml (2 hunks)
• requirements.txt (1 hunks)

Files skipped from review due to trivial changes (5)

• .conda/meta.yaml
• .conda_mac/build.sh
• .conda_mac/condarc.yaml
• .conda_mac/meta.yaml
• requirements.txt

Additional comments not posted (6)

.github/workflows/build_manual.yml (6)

14-15: Branch trigger updated to include elizabeth/fix-mac-conda-build.

---

86-86: Saving BUILD_PATH as a GITHUB_ENV variable for Ubuntu.

---

94-94: Saving BUILD_PATH as a GITHUB_ENV variable for Windows.

---

102-102: Saving BUILD_PATH as a GITHUB_ENV variable for Mac.

---

104-137: Testing built conda package for Ubuntu and Windows.

---

138-170: Testing built conda package for Mac.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 74.11%. Comparing base (7ed1229) to head (d084f74).
Report is 6 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1776      +/-   ##
===========================================
+ Coverage    73.30%   74.11%   +0.80%     
===========================================
  Files          134      134              
  Lines        24087    24462     +375     
===========================================
+ Hits         17658    18131     +473     
+ Misses        6429     6331      -98     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[coderabbitai]

Actionable comments posted: 0

Review Details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 5d576ac and b6cbdba.

Files selected for processing (2)

• .github/workflows/build.yml (1 hunks)
• sleap/version.py (1 hunks)

Files skipped from review due to trivial changes (2)

• .github/workflows/build.yml
• sleap/version.py

[coderabbitai]

Actionable comments posted: 0

Review Details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between b6cbdba and a72202a.

Files selected for processing (1)

• .github/workflows/build.yml (1 hunks)

Additional comments not posted (1)

.github/workflows/build.yml (1)

87-154: Ensure consistency in environment setup across OS platforms.

Verification successful

---

Ensure consistency in environment setup across OS platforms.

The environment setup and testing steps for Ubuntu/Windows and Mac are consistent. Both sections follow the same sequence of commands for creating and testing the conda environment with the sleap package. The only difference is the channels used in the conda create command, which is expected due to platform-specific dependencies.

• Ubuntu/Windows uses: -c file://$BUILD_PATH -c sleap/label/dev -c conda-forge -c nvidia -c anaconda
• Mac uses: -c file://$BUILD_PATH -c conda-forge -c anaconda

This difference is necessary and does not indicate inconsistency in the overall setup process.

Scripts Executed

The following scripts were executed for the analysis:

---

Script:

#!/bin/bash
# Description: Verify that the environment setup and testing steps are consistent across different OS platforms in the workflow file.

# Test: Search for inconsistencies in environment setup and testing steps. Expect: Uniform steps across all OS platforms.
rg --type yaml $'echo "Creating and testing conda environment with sleap package..."' .github/workflows/build.yml

Length of output: 270

---

---

Script:

#!/bin/bash
# Extract and compare the environment setup and testing steps for Ubuntu/Windows and Mac in the workflow file.

# Extract the Ubuntu/Windows section
ubuntu_windows_section=$(sed -n '/# Test built conda package (Ubuntu and Windows)/,/# Test built conda package (Mac)/p' .github/workflows/build.yml)

# Extract the Mac section
mac_section=$(sed -n '/# Test built conda package (Mac)/,$p' .github/workflows/build.yml)

# Output the sections for comparison
echo "Ubuntu/Windows Section:"
echo "$ubuntu_windows_section"
echo
echo "Mac Section:"
echo "$mac_section"

Length of output: 16897

[coderabbitai]

Actionable comments posted: 0

Review Details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between a72202a and b98594c.

Files selected for processing (2)

• .github/workflows/build_ci.yml (1 hunks)
• .github/workflows/build_manual.yml (2 hunks)

Files skipped from review due to trivial changes (1)

• .github/workflows/build_ci.yml

Files skipped from review as they are similar to previous changes (1)

• .github/workflows/build_manual.yml

[coderabbitai]

Actionable comments posted: 0

Review Details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between b98594c and d084f74.

Files selected for processing (1)

• .github/workflows/build_ci.yml (2 hunks)

Files skipped from review as they are similar to previous changes (1)

• .github/workflows/build_ci.yml