From fd66b87f2f3f5aa6ede2f3d6865365eafb04cfe2 Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Mon, 19 Feb 2024 16:22:06 -0700
Subject: [PATCH 1/3] refactoring build space step in test metapkg & kicking
 off tiny Prepare for testing purposes

---
 .../ci-distro-trial_3-test-metapackage.yaml   | 85 ++++---------------
 2024.5/tiny/passed/seed-environment-conda.yml |  1 +
 2 files changed, 16 insertions(+), 70 deletions(-)

diff --git a/.github/workflows/ci-distro-trial_3-test-metapackage.yaml b/.github/workflows/ci-distro-trial_3-test-metapackage.yaml
index 1a454652..0c014b53 100644
--- a/.github/workflows/ci-distro-trial_3-test-metapackage.yaml
+++ b/.github/workflows/ci-distro-trial_3-test-metapackage.yaml
@@ -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
@@ -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
@@ -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 }}"]'
 
diff --git a/2024.5/tiny/passed/seed-environment-conda.yml b/2024.5/tiny/passed/seed-environment-conda.yml
index 985318af..155d8340 100644
--- a/2024.5/tiny/passed/seed-environment-conda.yml
+++ b/2024.5/tiny/passed/seed-environment-conda.yml
@@ -1,3 +1,4 @@
+# adding comment to kick off CI
 channels:
 - https://packages.qiime2.org/qiime2/2024.5/tiny/passed
 - conda-forge

From e571d031823f956aac96c1b957b1b87b3dd5d5a7 Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Mon, 19 Feb 2024 17:04:14 -0700
Subject: [PATCH 2/3] fixing tiny seed env

---
 2024.5/tiny/passed/seed-environment-conda.yml | 5 ++---
 2024.5/tiny/staged/seed-environment-conda.yml | 4 ++--
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/2024.5/tiny/passed/seed-environment-conda.yml b/2024.5/tiny/passed/seed-environment-conda.yml
index 155d8340..deb91ec1 100644
--- a/2024.5/tiny/passed/seed-environment-conda.yml
+++ b/2024.5/tiny/passed/seed-environment-conda.yml
@@ -1,6 +1,5 @@
-# adding comment to kick off CI
 channels:
-- https://packages.qiime2.org/qiime2/2024.5/tiny/passed
+- https://packages.qiime2.org/qiime2/2024.2/tiny/released
 - conda-forge
 - bioconda
 - defaults
@@ -25,4 +24,4 @@ dependencies:
 - unifrac=1.3
 extras:
   variant_override:
-    qiime2_epoch: '2024.2'
+    qiime2_epoch: '2024.5'
diff --git a/2024.5/tiny/staged/seed-environment-conda.yml b/2024.5/tiny/staged/seed-environment-conda.yml
index 3dd35ec0..deb91ec1 100644
--- a/2024.5/tiny/staged/seed-environment-conda.yml
+++ b/2024.5/tiny/staged/seed-environment-conda.yml
@@ -1,5 +1,5 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.5/tiny/staged
+- https://packages.qiime2.org/qiime2/2024.2/tiny/released
 - conda-forge
 - bioconda
 - defaults
@@ -24,4 +24,4 @@ dependencies:
 - unifrac=1.3
 extras:
   variant_override:
-    qiime2_epoch: '2024.2'
+    qiime2_epoch: '2024.5'

From bf790d720d52743887c9cec32be7e3fa3e6e9c88 Mon Sep 17 00:00:00 2001
From: q2d2 <q2d2.noreply@gmail.com>
Date: Tue, 20 Feb 2024 00:54:00 +0000
Subject: [PATCH 3/3] Update conda environments (Prepare-tiny-2024.5)

---
 .../passed/qiime2-tiny-macos-latest-conda.yml | 26 +++++++++----------
 .../qiime2-tiny-ubuntu-latest-conda.yml       | 26 +++++++++----------
 2024.5/tiny/passed/seed-environment-conda.yml | 10 +++----
 2024.5/tiny/staged/seed-environment-conda.yml | 10 +++----
 4 files changed, 36 insertions(+), 36 deletions(-)

diff --git a/2024.5/tiny/passed/qiime2-tiny-macos-latest-conda.yml b/2024.5/tiny/passed/qiime2-tiny-macos-latest-conda.yml
index c7cf3382..84fd0e05 100644
--- a/2024.5/tiny/passed/qiime2-tiny-macos-latest-conda.yml
+++ b/2024.5/tiny/passed/qiime2-tiny-macos-latest-conda.yml
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git a/2024.5/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml b/2024.5/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml
index dacb82c1..7459695a 100644
--- a/2024.5/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml
+++ b/2024.5/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml
@@ -1,5 +1,5 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.2/tiny/passed
+- https://packages.qiime2.org/qiime2/2024.5/tiny/passed
 - bioconda
 - conda-forge
 - defaults
@@ -7,7 +7,7 @@ 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git a/2024.5/tiny/passed/seed-environment-conda.yml b/2024.5/tiny/passed/seed-environment-conda.yml
index deb91ec1..17c99a06 100644
--- a/2024.5/tiny/passed/seed-environment-conda.yml
+++ b/2024.5/tiny/passed/seed-environment-conda.yml
@@ -1,5 +1,5 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.2/tiny/released
+- https://packages.qiime2.org/qiime2/2024.5/tiny/passed
 - conda-forge
 - bioconda
 - defaults
@@ -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
diff --git a/2024.5/tiny/staged/seed-environment-conda.yml b/2024.5/tiny/staged/seed-environment-conda.yml
index deb91ec1..16d72a0a 100644
--- a/2024.5/tiny/staged/seed-environment-conda.yml
+++ b/2024.5/tiny/staged/seed-environment-conda.yml
@@ -1,5 +1,5 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.2/tiny/released
+- https://packages.qiime2.org/qiime2/2024.5/tiny/staged
 - conda-forge
 - bioconda
 - defaults
@@ -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