From 851952f5fbc1951d31ac082684c2638a52d311c0 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Fri, 15 Mar 2024 13:17:10 +0530
Subject: [PATCH 01/17] Add integration tests for galaxy packages using tpv

---
 .../test_galaxy_package_integration.yaml      | 44 +++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 .github/workflows/test_galaxy_package_integration.yaml

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
new file mode 100644
index 000000000000..ce57d94feed5
--- /dev/null
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -0,0 +1,44 @@
+name: Test Galaxy package integration with TPV
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10']
+    steps:
+      - name: Checkout galaxy code
+        uses: actions/checkout@v3
+      - name: Checkout tpv code
+        uses: actions/checkout@v3
+        with:
+          repository: galaxyproject/total-perspective-vortex
+          path: 'tpv'
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: replace tpv galaxy dependencies with local package paths from galaxy source
+        shell: bash
+        run: cat tpv/requirements_test.txt | sed -e '/^galaxy-/ s/-/_/g' | sed -E 's/^galaxy_(.*)$/\.\.\/packages\/\1/g;' > requirements_local.txt
+      - name: replace test requirements with updated requirements that point to local packages
+        run: mv requirements_local.txt tpv/requirements_test.txt
+      - name: Install required packages
+        run: pip install tox
+      - name: Run tox
+        run: tox -e py${{ matrix.python-version }}
+        env:
+          PYTHONUNBUFFERED: "True"
+        working-directory: 'tpv'

From f18dd1cb17ce6abffe0040bfa2d9f69677936b93 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Fri, 15 Mar 2024 17:21:24 +0530
Subject: [PATCH 02/17] display requirements prior to running tox

---
 .github/workflows/test_galaxy_package_integration.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index ce57d94feed5..c20e820315f7 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -35,6 +35,9 @@ jobs:
         run: cat tpv/requirements_test.txt | sed -e '/^galaxy-/ s/-/_/g' | sed -E 's/^galaxy_(.*)$/\.\.\/packages\/\1/g;' > requirements_local.txt
       - name: replace test requirements with updated requirements that point to local packages
         run: mv requirements_local.txt tpv/requirements_test.txt
+      - name: Display requirement contents
+        run: cat requirements_test.txt
+        working-directory: 'tpv'
       - name: Install required packages
         run: pip install tox
       - name: Run tox

From 51a88cec1f682ed611a76db80255b1cd8c2ff8ff Mon Sep 17 00:00:00 2001
From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
Date: Sun, 17 Mar 2024 10:33:45 +0530
Subject: [PATCH 03/17] code review suggestion - one-step sed and cat

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 .github/workflows/test_galaxy_package_integration.yaml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index c20e820315f7..2b409b613a50 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -31,12 +31,9 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: replace tpv galaxy dependencies with local package paths from galaxy source
-        shell: bash
-        run: cat tpv/requirements_test.txt | sed -e '/^galaxy-/ s/-/_/g' | sed -E 's/^galaxy_(.*)$/\.\.\/packages\/\1/g;' > requirements_local.txt
-      - name: replace test requirements with updated requirements that point to local packages
-        run: mv requirements_local.txt tpv/requirements_test.txt
-      - name: Display requirement contents
-        run: cat requirements_test.txt
+        run: |
+          sed -i'' -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1|' tpv/requirements_test.txt
+          cat tpv/requirements_test.txt
         working-directory: 'tpv'
       - name: Install required packages
         run: pip install tox

From ff94decf8008dd5a75a66ef7b84464ad51672421 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 01:15:05 +0530
Subject: [PATCH 04/17] Use locally built wheels

---
 .github/workflows/test_galaxy_package_integration.yaml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index 2b409b613a50..bc74842a8d35 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -30,11 +30,13 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-      - name: replace tpv galaxy dependencies with local package paths from galaxy source
+      - name: replace tpv galaxy dependencies with package paths from local galaxy build
         run: |
-          sed -i'' -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1|' tpv/requirements_test.txt
+          # create local release
+          echo "c" | ./scripts/release.sh -l
+          # make requirements point to local wheels
+          sed -i'' -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1/build/\*.whl|' tpv/requirements_test.txt
           cat tpv/requirements_test.txt
-        working-directory: 'tpv'
       - name: Install required packages
         run: pip install tox
       - name: Run tox

From e088136b869497416136041e8d6f0b675f6b842b Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 01:18:05 +0530
Subject: [PATCH 05/17] Setup venv prior to creating release

---
 .github/workflows/test_galaxy_package_integration.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index bc74842a8d35..28daa54aebff 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -32,6 +32,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: replace tpv galaxy dependencies with package paths from local galaxy build
         run: |
+          make setup-venv
           # create local release
           echo "c" | ./scripts/release.sh -l
           # make requirements point to local wheels

From 9a401c770a65014d9ba7553108003ccd1d5758a3 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 01:31:55 +0530
Subject: [PATCH 06/17] Add pip caching and skip client build

---
 .../workflows/test_galaxy_package_integration.yaml   | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index 28daa54aebff..5d1ed30115be 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -30,9 +30,19 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Cache pip dir
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v3
+        with:
+          path: '.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('requirements.txt') }}-integration
       - name: replace tpv galaxy dependencies with package paths from local galaxy build
         run: |
-          make setup-venv
+          GALAXY_SKIP_CLIENT_BUILD=1 make setup-venv
           # create local release
           echo "c" | ./scripts/release.sh -l
           # make requirements point to local wheels

From ed2180ca86c87daad9c8e7e9fa67258aef3f0892 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 01:49:43 +0530
Subject: [PATCH 07/17] Get full python version in action

---
 .github/workflows/test_galaxy_package_integration.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index 5d1ed30115be..305558fdf324 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -30,6 +30,10 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
         uses: actions/cache@v3
         with:

From b4cf0a640e3e63d2816959f83f2d121fe723cd76 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 01:50:03 +0530
Subject: [PATCH 08/17] correct build directory

---
 .github/workflows/test_galaxy_package_integration.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index 305558fdf324..7f588c61edd7 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -50,7 +50,7 @@ jobs:
           # create local release
           echo "c" | ./scripts/release.sh -l
           # make requirements point to local wheels
-          sed -i'' -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1/build/\*.whl|' tpv/requirements_test.txt
+          sed -i'' -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1/dist/\*.whl|' tpv/requirements_test.txt
           cat tpv/requirements_test.txt
       - name: Install required packages
         run: pip install tox

From 5064e5bf6c9bed689d26490b694ca85592fab72b Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 11:57:38 +0530
Subject: [PATCH 09/17] Use full path to local wheels

---
 .../workflows/test_galaxy_package_integration.yaml  | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index 7f588c61edd7..82ad8defbf1c 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -50,8 +50,17 @@ jobs:
           # create local release
           echo "c" | ./scripts/release.sh -l
           # make requirements point to local wheels
-          sed -i'' -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1/dist/\*.whl|' tpv/requirements_test.txt
-          cat tpv/requirements_test.txt
+          while read -r line; do
+            package_path=`echo $line | sed -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1|'`
+            if [ -d $package_path ]; then
+              row=`find $package_path/dist -type d -exec find {} -depth -maxdepth 1 -type f -name '*.whl' -print -quit \;`
+            else
+              row=$line
+            fi
+            echo $row >> tpv/requirements_local.txt
+          done < "$file"
+          cat tpv/requirements_local.txt
+          mv tpv/requirements_local.txt tpv/requirements_test.txt
       - name: Install required packages
         run: pip install tox
       - name: Run tox

From ca97701ca41f87f034969d3c82876a6dd53980d5 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 12:12:27 +0530
Subject: [PATCH 10/17] Skip node when building venv

---
 .github/workflows/test_galaxy_package_integration.yaml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index 82ad8defbf1c..3ab7a1387eaf 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -46,15 +46,17 @@ jobs:
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('requirements.txt') }}-integration
       - name: replace tpv galaxy dependencies with package paths from local galaxy build
         run: |
-          GALAXY_SKIP_CLIENT_BUILD=1 make setup-venv
+          GALAXY_SKIP_NODE=1 GALAXY_SKIP_CLIENT_BUILD=1 make setup-venv
           # create local release
           echo "c" | ./scripts/release.sh -l
           # make requirements point to local wheels
           while read -r line; do
-            package_path=`echo $line | sed -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1|'`
+            package_path=`echo $line | sed -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1|'`            
             if [ -d $package_path ]; then
+              # This is a local package. Replace it with the path to the local wheel
               row=`find $package_path/dist -type d -exec find {} -depth -maxdepth 1 -type f -name '*.whl' -print -quit \;`
             else
+              # pass original requirement line unchanged
               row=$line
             fi
             echo $row >> tpv/requirements_local.txt

From cdd582482d81cf9149946298dee75a81a059b400 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 12:35:01 +0530
Subject: [PATCH 11/17] Fix typo

---
 .github/workflows/test_galaxy_package_integration.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index 3ab7a1387eaf..81566864dbaa 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -44,12 +44,12 @@ jobs:
         with:
           path: '.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('requirements.txt') }}-integration
-      - name: replace tpv galaxy dependencies with package paths from local galaxy build
+      - name: Replace tpv galaxy dependencies with package paths from local galaxy build
         run: |
           GALAXY_SKIP_NODE=1 GALAXY_SKIP_CLIENT_BUILD=1 make setup-venv
           # create local release
           echo "c" | ./scripts/release.sh -l
-          # make requirements point to local wheels
+          # make requirements point to local wheels where possible
           while read -r line; do
             package_path=`echo $line | sed -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1|'`            
             if [ -d $package_path ]; then

From 22932e3a92ca0863817850cbd24706c8315fe1aa Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 12:58:30 +0530
Subject: [PATCH 12/17] Don't presist credentials when checking out tpv

---
 .github/workflows/test_galaxy_package_integration.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index 81566864dbaa..ce5a8b98bf3d 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -20,13 +20,14 @@ jobs:
       matrix:
         python-version: ['3.10']
     steps:
-      - name: Checkout galaxy code
-        uses: actions/checkout@v3
       - name: Checkout tpv code
         uses: actions/checkout@v3
         with:
           repository: galaxyproject/total-perspective-vortex
           path: 'tpv'
+          persist-credentials: false
+      - name: Checkout galaxy code
+        uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}

From 98a2c22c7283dc90f7c2fbf0cf4b83824d21a1b6 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 13:09:42 +0530
Subject: [PATCH 13/17] Force https on checkout

---
 scripts/release.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/release.sh b/scripts/release.sh
index a76596eb9f46..d8ec0c0d23ec 100755
--- a/scripts/release.sh
+++ b/scripts/release.sh
@@ -8,7 +8,7 @@ shopt -s extglob
 : ${VENV:=.venv}
 : ${FORK_REMOTE:=origin}
 : ${UPSTREAM_REMOTE:=upstream}
-: ${UPSTREAM_REMOTE_URL:=git@github.com:galaxyproject/galaxy.git}
+: ${UPSTREAM_REMOTE_URL:=https://github.com/galaxyproject/galaxy.git}
 : ${DEV_BRANCH:=dev}
 : ${STABLE_BRANCH:=master}
 

From 0098d634df865bc60399cc21cb987be606225004 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 13:44:49 +0530
Subject: [PATCH 14/17] Fix unbound var

---
 .github/workflows/test_galaxy_package_integration.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index ce5a8b98bf3d..d44055eff2a5 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -61,7 +61,7 @@ jobs:
               row=$line
             fi
             echo $row >> tpv/requirements_local.txt
-          done < "$file"
+          done < "tpv/requirements_test.txt"
           cat tpv/requirements_local.txt
           mv tpv/requirements_local.txt tpv/requirements_test.txt
       - name: Install required packages

From f79d7c669be4dd04e47aac8b1c9bab0c397e0d05 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 14:04:27 +0530
Subject: [PATCH 15/17] refactor script and fix path

---
 .../test_galaxy_package_integration.yaml      | 25 ++++++++++---------
 scripts/release.sh                            |  2 +-
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index d44055eff2a5..3e7d4fd917ff 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -20,14 +20,13 @@ jobs:
       matrix:
         python-version: ['3.10']
     steps:
+      - name: Checkout galaxy code
+        uses: actions/checkout@v3
       - name: Checkout tpv code
         uses: actions/checkout@v3
         with:
           repository: galaxyproject/total-perspective-vortex
           path: 'tpv'
-          persist-credentials: false
-      - name: Checkout galaxy code
-        uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
@@ -49,21 +48,23 @@ jobs:
         run: |
           GALAXY_SKIP_NODE=1 GALAXY_SKIP_CLIENT_BUILD=1 make setup-venv
           # create local release
-          echo "c" | ./scripts/release.sh -l
+          echo "c" | UPSTREAM_REMOTE_URL="https://github.com/galaxyproject/galaxy.git" ./scripts/release.sh -l
           # make requirements point to local wheels where possible
-          while read -r line; do
-            package_path=`echo $line | sed -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1|'`            
-            if [ -d $package_path ]; then
+          cd tpv
+          while IFS= read -r line; do
+            # Handle galaxy- packages specifically
+            package_path=`echo $line | sed -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1|'`
+            if [ -d "$package_path" ]; then
               # This is a local package. Replace it with the path to the local wheel
               row=`find $package_path/dist -type d -exec find {} -depth -maxdepth 1 -type f -name '*.whl' -print -quit \;`
             else
               # pass original requirement line unchanged
-              row=$line
+              row="$line"
             fi
-            echo $row >> tpv/requirements_local.txt
-          done < "tpv/requirements_test.txt"
-          cat tpv/requirements_local.txt
-          mv tpv/requirements_local.txt tpv/requirements_test.txt
+            echo "$row" >> requirements_local.txt
+          done < "requirements_test.txt"
+          cat requirements_local.txt
+          mv requirements_local.txt requirements_test.txt
       - name: Install required packages
         run: pip install tox
       - name: Run tox
diff --git a/scripts/release.sh b/scripts/release.sh
index d8ec0c0d23ec..a76596eb9f46 100755
--- a/scripts/release.sh
+++ b/scripts/release.sh
@@ -8,7 +8,7 @@ shopt -s extglob
 : ${VENV:=.venv}
 : ${FORK_REMOTE:=origin}
 : ${UPSTREAM_REMOTE:=upstream}
-: ${UPSTREAM_REMOTE_URL:=https://github.com/galaxyproject/galaxy.git}
+: ${UPSTREAM_REMOTE_URL:=git@github.com:galaxyproject/galaxy.git}
 : ${DEV_BRANCH:=dev}
 : ${STABLE_BRANCH:=master}
 

From bdcad791bb53668396cb159ea17d2ae52533664b Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 25 Mar 2024 19:44:09 +0530
Subject: [PATCH 16/17] simplify find by assuming one wheel per folder

---
 .github/workflows/test_galaxy_package_integration.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index 3e7d4fd917ff..7e49239afe71 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -56,7 +56,7 @@ jobs:
             package_path=`echo $line | sed -e '/^galaxy-/ s/-/_/g' -e 's|^galaxy_\(.*\)$|../packages/\1|'`
             if [ -d "$package_path" ]; then
               # This is a local package. Replace it with the path to the local wheel
-              row=`find $package_path/dist -type d -exec find {} -depth -maxdepth 1 -type f -name '*.whl' -print -quit \;`
+              row=`find $package_path/dist -type f -name '*.whl'`
             else
               # pass original requirement line unchanged
               row="$line"

From 0765c313f7c1a277c69418f4030da9572a7692e4 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Mon, 3 Jun 2024 19:40:43 +0530
Subject: [PATCH 17/17] Test failure

---
 .../test_galaxy_package_integration.yaml      | 24 +++++++++----------
 packages/app/MANIFEST.in                      |  1 -
 2 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/test_galaxy_package_integration.yaml b/.github/workflows/test_galaxy_package_integration.yaml
index 7e49239afe71..230d205ed113 100644
--- a/.github/workflows/test_galaxy_package_integration.yaml
+++ b/.github/workflows/test_galaxy_package_integration.yaml
@@ -34,21 +34,21 @@ jobs:
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
-      - name: Cache galaxy venv
-        uses: actions/cache@v3
-        with:
-          path: '.venv'
-          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('requirements.txt') }}-integration
+      # - name: Cache pip dir
+      #   uses: actions/cache@v3
+      #   with:
+      #     path: ~/.cache/pip
+      #     key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+      # - name: Cache galaxy venv
+      #   uses: actions/cache@v3
+      #   with:
+      #     path: '.venv'
+      #     key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('requirements.txt') }}-integration
       - name: Replace tpv galaxy dependencies with package paths from local galaxy build
         run: |
           GALAXY_SKIP_NODE=1 GALAXY_SKIP_CLIENT_BUILD=1 make setup-venv
           # create local release
-          echo "c" | UPSTREAM_REMOTE_URL="https://github.com/galaxyproject/galaxy.git" ./scripts/release.sh -l
+          echo "c" | UPSTREAM_REMOTE_URL="https://github.com/nuwang/galaxy.git" ./scripts/release.sh -l
           # make requirements point to local wheels where possible
           cd tpv
           while IFS= read -r line; do
@@ -68,7 +68,7 @@ jobs:
       - name: Install required packages
         run: pip install tox
       - name: Run tox
-        run: tox -e py${{ matrix.python-version }}
+        run: tox -e py${{ matrix.python-version }} -- --runslow
         env:
           PYTHONUNBUFFERED: "True"
         working-directory: 'tpv'
diff --git a/packages/app/MANIFEST.in b/packages/app/MANIFEST.in
index 31845ffa0b10..d430c3fc088a 100644
--- a/packages/app/MANIFEST.in
+++ b/packages/app/MANIFEST.in
@@ -1,5 +1,4 @@
 include *.rst *.txt LICENSE */py.typed
-include galaxy/carbon_emissions/carbon_intensity.csv
 include galaxy/dependencies/*.txt
 include galaxy/dependencies/*.sh
 include galaxy/jobs/runners/util/job_script/*.sh