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PREP: 2024.5 (tiny) & some GHA refactors #155

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merged 3 commits into from
Feb 20, 2024
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PREP: 2024.5 (tiny) & some GHA refactors #155

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fd66b87
refactoring build space step in test metapkg & kicking off tiny Prepa…
lizgehret Feb 19, 2024
e571d03
fixing tiny seed env
lizgehret Feb 20, 2024
bf790d7
Update conda environments (Prepare-tiny-2024.5)
q2d2 Feb 20, 2024
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85 changes: 15 additions & 70 deletions .github/workflows/ci-distro-trial_3-test-metapackage.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -40,14 +40,15 @@ jobs:
run: |
echo "matrix=$(cat ${{ env.matrix_path }}/retest_matrix.json)" >> $GITHUB_OUTPUT

run_matrix_ubuntu:
name: '${{ matrix.package }} (ubuntu-latest)'
run_matrix:
name: '${{ matrix.package }} (${{ matrix.os }})'
needs: configure_matrix
strategy:
fail-fast: false
matrix:
package: ${{ fromJSON(needs.configure_matrix.outputs.matrix) }}
runs-on: ubuntu-latest
os: [ubuntu-latest, macos-latest]
runs-on: ${{ matrix.os }}
steps:
- name: get environment path
uses: actions/download-artifact@v3
Expand All @@ -67,80 +68,24 @@ jobs:
name: ${{ inputs.rebuilt-channel-key }}
path: ${{ env.rebuilt_channel_path }}

- name: Free Disk Space (Ubuntu)
uses: jlumbroso/free-disk-space@main
with:
# this might remove tools that are actually needed,
# if set to "true" but frees about 6 GB
tool-cache: false

android: true
dotnet: true
haskell: true
large-packages: true
docker-images: true
swap-storage: true

- name: install environment
id: env
uses: qiime2/action-library-packaging/create-env@beta
with:
conda-prefix: './test-env'
environment-file: ${{ env.solved_environment_path }}/${{ inputs.distro-name }}-ubuntu-latest-conda.yml

- name: run qiime info
- name: Maximize build space for linux
shell: bash
if: ${{ runner.os == 'Linux' }}
run: |
${{ steps.env.outputs.conda-activate }}
qiime info

- name: 'collect package path'
id: 'collect-package'
uses: qiime2/action-library-packaging/collect-package@beta
with:
runner: ubuntu-latest
package: ${{ matrix.package }}
channels: '["${{ env.rebuilt_channel_path }}", "${{ env.patched_channel_path }}"]'

- name: 'run tests'
uses: qiime2/action-library-packaging/test-package@beta
with:
conda-activate: ${{ steps.env.outputs.conda-activate }}
package-path: ${{ steps.collect-package.outputs.path }}

run_matrix_osx:
name: '${{ matrix.package }} (macos-latest)'
needs: configure_matrix
strategy:
fail-fast: false
matrix:
package: ${{ fromJSON(needs.configure_matrix.outputs.matrix) }}
runs-on: macos-latest
steps:
- name: get environment path
uses: actions/download-artifact@v3
with:
name: ${{ inputs.solved-environment-key }}
path: ${{ env.solved_environment_path }}

- name: 'Fetch base channel with patches'
uses: actions/download-artifact@v3
with:
name: ${{ inputs.patched-channel-key }}
path: ${{ env.patched_channel_path }}

- name: 'Fetch rebuilt channel'
uses: actions/download-artifact@v3
with:
name: ${{ inputs.rebuilt-channel-key }}
path: ${{ env.rebuilt_channel_path }}
echo "Removing unwanted software... "
sudo rm -rf /usr/share/dotnet
sudo rm -rf /usr/local/lib/android
sudo rm -rf /opt/ghc
sudo rm -rf /opt/hostedtoolcache/CodeQL
sudo docker image prune --all --force
echo "... done"

- name: install environment
id: env
uses: qiime2/action-library-packaging/create-env@beta
with:
conda-prefix: './test-env'
environment-file: ${{ env.solved_environment_path }}/${{ inputs.distro-name }}-macos-latest-conda.yml
environment-file: ${{ env.solved_environment_path }}/${{ inputs.distro-name }}-${{ matrix.os }}-conda.yml

- name: run qiime info
shell: bash
Expand All @@ -152,7 +97,7 @@ jobs:
id: 'collect-package'
uses: qiime2/action-library-packaging/collect-package@beta
with:
runner: macos-latest
runner: ${{ matrix.os }}
package: ${{ matrix.package }}
channels: '["${{ env.rebuilt_channel_path }}", "${{ env.patched_channel_path }}"]'

Expand Down
26 changes: 13 additions & 13 deletions 2024.5/tiny/passed/qiime2-tiny-macos-latest-conda.yml
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
channels:
- https://packages.qiime2.org/qiime2/2024.2/tiny/passed
- https://packages.qiime2.org/qiime2/2024.5/tiny/passed
- bioconda
- conda-forge
- defaults
dependencies:
- _r-mutex=1.0.1
- anyio=4.2.0
- anyio=4.3.0
- appdirs=1.4.4
- appnope=0.1.4
- argon2-cffi=23.1.0
Expand Down Expand Up @@ -169,9 +169,9 @@ dependencies:
- natsort=8.4.0
- nbclassic=1.0.0
- nbclient=0.8.0
- nbconvert=7.16.0
- nbconvert-core=7.16.0
- nbconvert-pandoc=7.16.0
- nbconvert=7.16.1
- nbconvert-core=7.16.1
- nbconvert-pandoc=7.16.1
- nbformat=5.9.2
- ncurses=6.4
- nest-asyncio=1.6.0
Expand All @@ -184,7 +184,7 @@ dependencies:
- overrides=7.7.0
- packaging=23.2
- pandas=1.5.3
- pandoc=3.1.12
- pandoc=3.1.12.1
- pandocfilters=1.5.0
- pango=1.50.14
- paramiko=3.4.0
Expand Down Expand Up @@ -224,10 +224,10 @@ dependencies:
- pytz=2024.1
- pyyaml=6.0.1
- pyzmq=24.0.1
- q2-mystery-stew=2024.2.0
- q2-types=2024.2.0
- q2cli=2024.2.0
- qiime2=2024.2.0
- q2-mystery-stew=2024.5.0.dev0
- q2-types=2024.5.0.dev0
- q2cli=2024.5.0.dev0
- qiime2=2024.5.0.dev0
- r-base=4.2.3
- readline=8.2
- referencing=0.33.0
Expand All @@ -241,7 +241,7 @@ dependencies:
- scipy=1.10.0
- send2trash=1.8.2
- setproctitle=1.3.3
- setuptools=69.0.3
- setuptools=69.1.0
- sigtool=0.1.3
- six=1.16.0
- sniffio=1.3.0
Expand All @@ -256,7 +256,7 @@ dependencies:
- tktable=2.10
- tomli=2.0.1
- tomlkit=0.12.3
- tornado=6.3.3
- tornado=6.4
- traitlets=5.9.0
- typeguard=2.13.3
- types-python-dateutil=2.8.19.20240106
Expand All @@ -268,7 +268,7 @@ dependencies:
- unifrac=1.3
- unifrac-binaries=1.3.2
- uri-template=1.3.0
- urllib3=2.2.0
- urllib3=2.2.1
- wcwidth=0.2.13
- webcolors=1.13
- webencodings=0.5.1
Expand Down
26 changes: 13 additions & 13 deletions 2024.5/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
channels:
- https://packages.qiime2.org/qiime2/2024.2/tiny/passed
- https://packages.qiime2.org/qiime2/2024.5/tiny/passed
- bioconda
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1
- _openmp_mutex=4.5
- _r-mutex=1.0.1
- anyio=4.2.0
- anyio=4.3.0
- appdirs=1.4.4
- argon2-cffi=23.1.0
- argon2-cffi-bindings=21.2.0
Expand Down Expand Up @@ -162,9 +162,9 @@ dependencies:
- natsort=8.4.0
- nbclassic=1.0.0
- nbclient=0.8.0
- nbconvert=7.16.0
- nbconvert-core=7.16.0
- nbconvert-pandoc=7.16.0
- nbconvert=7.16.1
- nbconvert-core=7.16.1
- nbconvert-pandoc=7.16.1
- nbformat=5.9.2
- ncurses=6.4
- nest-asyncio=1.6.0
Expand All @@ -177,7 +177,7 @@ dependencies:
- overrides=7.7.0
- packaging=23.2
- pandas=1.5.3
- pandoc=3.1.12
- pandoc=3.1.12.1
- pandocfilters=1.5.0
- pango=1.50.14
- paramiko=3.4.0
Expand Down Expand Up @@ -215,10 +215,10 @@ dependencies:
- pytz=2024.1
- pyyaml=6.0.1
- pyzmq=24.0.1
- q2-mystery-stew=2024.2.0
- q2-types=2024.2.0
- q2cli=2024.2.0
- qiime2=2024.2.0
- q2-mystery-stew=2024.5.0.dev0
- q2-types=2024.5.0.dev0
- q2cli=2024.5.0.dev0
- qiime2=2024.5.0.dev0
- r-base=4.2.3
- readline=8.2
- referencing=0.33.0
Expand All @@ -233,7 +233,7 @@ dependencies:
- sed=4.8
- send2trash=1.8.2
- setproctitle=1.3.3
- setuptools=69.0.3
- setuptools=69.1.0
- six=1.16.0
- sniffio=1.3.0
- soupsieve=2.5
Expand All @@ -247,7 +247,7 @@ dependencies:
- tktable=2.10
- tomli=2.0.1
- tomlkit=0.12.3
- tornado=6.3.3
- tornado=6.4
- traitlets=5.9.0
- typeguard=2.13.3
- types-python-dateutil=2.8.19.20240106
Expand All @@ -259,7 +259,7 @@ dependencies:
- unifrac=1.3
- unifrac-binaries=1.3.2
- uri-template=1.3.0
- urllib3=2.2.0
- urllib3=2.2.1
- wcwidth=0.2.13
- webcolors=1.13
- webencodings=0.5.1
Expand Down
10 changes: 5 additions & 5 deletions 2024.5/tiny/passed/seed-environment-conda.yml
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Expand Up @@ -12,10 +12,10 @@ dependencies:
- pandas=1.5.3
- parsl=2023.12.04
- python=3.8
- q2-mystery-stew=2024.2.0
- q2-types=2024.2.0
- q2cli=2024.2.0
- qiime2=2024.2.0
- q2-mystery-stew=2024.5.0.dev0
- q2-types=2024.5.0.dev0
- q2cli=2024.5.0.dev0
- qiime2=2024.5.0.dev0
- r-base=4.2.2
- scikit-bio=0.5.8
- scikit-learn=0.24.1
Expand All @@ -24,4 +24,4 @@ dependencies:
- unifrac=1.3
extras:
variant_override:
qiime2_epoch: '2024.2'
qiime2_epoch: '2024.5'
10 changes: 5 additions & 5 deletions 2024.5/tiny/staged/seed-environment-conda.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,10 @@ dependencies:
- pandas=1.5.3
- parsl=2023.12.04
- python=3.8
- q2-mystery-stew=2024.2.0
- q2-types=2024.2.0
- q2cli=2024.2.0
- qiime2=2024.2.0
- q2-mystery-stew=2024.5.0.dev0
- q2-types=2024.5.0.dev0
- q2cli=2024.5.0.dev0
- qiime2=2024.5.0.dev0
- r-base=4.2.2
- scikit-bio=0.5.8
- scikit-learn=0.24.1
Expand All @@ -24,4 +24,4 @@ dependencies:
- unifrac=1.3
extras:
variant_override:
qiime2_epoch: '2024.2'
qiime2_epoch: '2024.5'