From 8dd96b2a9da2279e885c94feaeb7f95d6f4e6687 Mon Sep 17 00:00:00 2001
From: Nils Homer <nh13@users.noreply.github.com>
Date: Tue, 21 Jan 2025 21:34:56 -0700
Subject: [PATCH 1/7] ci: optimize fetch-depth in github actions

---
 .github/workflows/PR.yml             | 8 --------
 .github/workflows/build-failures.yml | 2 --
 .github/workflows/master.yml         | 9 ++++++---
 .github/workflows/nightly.yml        | 2 --
 4 files changed, 6 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/PR.yml b/.github/workflows/PR.yml
index 84fb230ad329f..b02598415bc00 100644
--- a/.github/workflows/PR.yml
+++ b/.github/workflows/PR.yml
@@ -14,8 +14,6 @@ jobs:
       max-parallel: 13
     steps:
       - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
@@ -61,8 +59,6 @@ jobs:
     needs: lint
     steps:
       - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
@@ -148,8 +144,6 @@ jobs:
     needs: build-linux
     steps:
       - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
@@ -220,8 +214,6 @@ jobs:
   #   needs: build-linux
   #   steps:
   #     - uses: actions/checkout@v4
-  #       with:
-  #         fetch-depth: 0
 
   #     # bail if there's no osx-arm64 recipes
   #     - name: Check for Additional Platforms
diff --git a/.github/workflows/build-failures.yml b/.github/workflows/build-failures.yml
index 49db9ce180f70..db3d555f82623 100644
--- a/.github/workflows/build-failures.yml
+++ b/.github/workflows/build-failures.yml
@@ -17,8 +17,6 @@ jobs:
     runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
diff --git a/.github/workflows/master.yml b/.github/workflows/master.yml
index b2f84cdc4f187..a2d2f6fd2db1b 100644
--- a/.github/workflows/master.yml
+++ b/.github/workflows/master.yml
@@ -12,9 +12,10 @@ jobs:
       fail-fast: false
       max-parallel: 13
     steps:
+      # Fetch the last two commits for the --git-range argument to bioconda-utils
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 0
+          fetch-depth: 2 
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
@@ -59,9 +60,10 @@ jobs:
       fail-fast: false
       max-parallel: 4
     steps:
+      # Fetch the last two commits for the --git-range argument to bioconda-utils
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 0
+          fetch-depth: 2
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
@@ -111,9 +113,10 @@ jobs:
   #     fail-fast: false
   #     max-parallel: 4
   #   steps:
+  #     # Fetch the last two commits for the --git-range argument to bioconda-utils
   #     - uses: actions/checkout@v4
   #       with:
-  #         fetch-depth: 0
+  #         fetch-depth: 2
 
   #     # bail if there's no osx-arm64 recipes
   #     - name: Check for Additional Platforms
diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
index 850a5d83fc5ad..bbafe03269845 100644
--- a/.github/workflows/nightly.yml
+++ b/.github/workflows/nightly.yml
@@ -12,8 +12,6 @@ jobs:
       max-parallel: 4
     steps:
       - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH

From 3924729ed4b4c9d9afa13cc74ee5b065cf563428 Mon Sep 17 00:00:00 2001
From: Nils Homer <nh13@users.noreply.github.com>
Date: Tue, 21 Jan 2025 22:24:52 -0700
Subject: [PATCH 2/7] Update PR.yml

---
 .github/workflows/PR.yml | 53 ++++++++++++++++++++++++++++++----------
 1 file changed, 40 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/PR.yml b/.github/workflows/PR.yml
index b02598415bc00..5f046770f564f 100644
--- a/.github/workflows/PR.yml
+++ b/.github/workflows/PR.yml
@@ -15,6 +15,19 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Set GITHUB_BASE_REF if not already set
+        id: github_base_ref
+        run: |
+          if [ -z "$GITHUB_BASE_REF" ] ; then
+              echo GITHUB_BASE_REF="master" >> $GITHUB_ENV     
+          fi
+  
+      - name: Fetch commits through the merge base
+        uses: BioData/fetch-through-merge-base@v0
+        with:
+          base_ref: ${{ env.GITHUB_BASE_REF }}
+          head_ref: ${{ github.sha }}
+
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
 
@@ -43,10 +56,6 @@ jobs:
           conda config --show-sources
           python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")'
           echo '============'
-          if [ -z "$GITHUB_BASE_REF" ] ; then
-              export GITHUB_BASE_REF="master"
-          fi
-          git fetch origin "$GITHUB_BASE_REF"
           bioconda-utils lint --loglevel debug --full-report --git-range origin/"$GITHUB_BASE_REF" HEAD
           conda clean -y --all
 
@@ -60,6 +69,20 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Set GITHUB_BASE_REF if not already set
+        id: github_base_ref
+        run: |
+          if [ -z "$GITHUB_BASE_REF" ] ; then
+              echo GITHUB_BASE_REF="master" >> $GITHUB_ENV     
+          fi
+  
+      - name: Fetch commits through the merge base
+        uses: BioData/fetch-through-merge-base@v0
+        with:
+          base_ref: ${{ env.GITHUB_BASE_REF }}
+          head_ref: ${{ github.sha }}
+
+
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
 
@@ -91,10 +114,6 @@ jobs:
           eval "$(conda shell.bash hook)"
           conda activate bioconda
           source common.sh
-          if [ -z "$GITHUB_BASE_REF" ] ; then
-              export GITHUB_BASE_REF="master"
-          fi
-          git fetch origin "$GITHUB_BASE_REF"
 
           bioconda-utils build recipes config.yml \
             --docker --mulled-test \
@@ -144,6 +163,19 @@ jobs:
     needs: build-linux
     steps:
       - uses: actions/checkout@v4
+      
+      - name: Set GITHUB_BASE_REF if not already set
+        id: github_base_ref
+        run: |
+          if [ -z "$GITHUB_BASE_REF" ] ; then
+              echo GITHUB_BASE_REF="master" >> $GITHUB_ENV     
+          fi
+  
+      - name: Fetch commits through the merge base
+        uses: BioData/fetch-through-merge-base@v0
+        with:
+          base_ref: ${{ env.GITHUB_BASE_REF }}
+          head_ref: ${{ github.sha }}
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
@@ -177,11 +209,6 @@ jobs:
               rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2
           done
 
-          if [ -z "$GITHUB_BASE_REF" ] ; then
-              export GITHUB_BASE_REF="master"
-          fi
-          git fetch origin "$GITHUB_BASE_REF"
-
           bioconda-utils build recipes config.yml \
             --git-range origin/"$GITHUB_BASE_REF" HEAD
 

From d51a162cf8380cddc5f297041c29462e50729898 Mon Sep 17 00:00:00 2001
From: Nils Homer <nh13@users.noreply.github.com>
Date: Tue, 21 Jan 2025 22:25:27 -0700
Subject: [PATCH 3/7] Update build-failures.yml

---
 .github/workflows/build-failures.yml | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-failures.yml b/.github/workflows/build-failures.yml
index db3d555f82623..9821dfe080257 100644
--- a/.github/workflows/build-failures.yml
+++ b/.github/workflows/build-failures.yml
@@ -18,6 +18,19 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Set GITHUB_BASE_REF if not already set
+        id: github_base_ref
+        run: |
+          if [ -z "$GITHUB_BASE_REF" ] ; then
+              echo GITHUB_BASE_REF="master" >> $GITHUB_ENV     
+          fi
+  
+      - name: Fetch commits through the merge base
+        uses: BioData/fetch-through-merge-base@v0
+        with:
+          base_ref: ${{ env.GITHUB_BASE_REF }}
+          head_ref: ${{ github.sha }}
+
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
 
@@ -58,10 +71,6 @@ jobs:
             echo "Automatically updated (nightly) list of build failures that currently block builds from the listed recipes. Please help with fixing them!" >> $md
             bioconda-utils list-build-failures recipes --output-format markdown --link-prefix https://github.com/bioconda/bioconda-recipes/blob/master >> $md
           else
-            if [ -z "$GITHUB_BASE_REF" ] ; then
-                export GITHUB_BASE_REF="master"
-            fi
-            git fetch origin "$GITHUB_BASE_REF"
             md="build-failures/build-failures-${branch}.md"
             echo "# Build failures on \`${branch}\`" > $md
             echo "Automatically updated list of build failures that currently block builds from the listed recipes on the \`${branch}\` branch." >> $md

From 949bd8508a456c546d8b2db840528a04ab43ca24 Mon Sep 17 00:00:00 2001
From: Nils Homer <nh13@users.noreply.github.com>
Date: Tue, 21 Jan 2025 22:35:07 -0700
Subject: [PATCH 4/7] debug

---
 .github/workflows/PR.yml             | 12 ++++++++----
 .github/workflows/build-failures.yml |  6 ++++--
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/PR.yml b/.github/workflows/PR.yml
index 5f046770f564f..7ba7f607d6e47 100644
--- a/.github/workflows/PR.yml
+++ b/.github/workflows/PR.yml
@@ -19,13 +19,15 @@ jobs:
         id: github_base_ref
         run: |
           if [ -z "$GITHUB_BASE_REF" ] ; then
-              echo GITHUB_BASE_REF="master" >> $GITHUB_ENV     
+              export GITHUB_BASE_REF="master"
+              export GITHUB_BASE_REF="${GITHUB_BASE_REF}" >> $GITHUB_ENV     
           fi
+          echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT
   
       - name: Fetch commits through the merge base
         uses: BioData/fetch-through-merge-base@v0
         with:
-          base_ref: ${{ env.GITHUB_BASE_REF }}
+          base_ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
           head_ref: ${{ github.sha }}
 
       - name: set path
@@ -73,13 +75,15 @@ jobs:
         id: github_base_ref
         run: |
           if [ -z "$GITHUB_BASE_REF" ] ; then
-              echo GITHUB_BASE_REF="master" >> $GITHUB_ENV     
+              export GITHUB_BASE_REF="master"
+              export GITHUB_BASE_REF="${GITHUB_BASE_REF}" >> $GITHUB_ENV     
           fi
+          echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT
   
       - name: Fetch commits through the merge base
         uses: BioData/fetch-through-merge-base@v0
         with:
-          base_ref: ${{ env.GITHUB_BASE_REF }}
+          base_ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
           head_ref: ${{ github.sha }}
 
 
diff --git a/.github/workflows/build-failures.yml b/.github/workflows/build-failures.yml
index 9821dfe080257..4197cfee555a9 100644
--- a/.github/workflows/build-failures.yml
+++ b/.github/workflows/build-failures.yml
@@ -22,13 +22,15 @@ jobs:
         id: github_base_ref
         run: |
           if [ -z "$GITHUB_BASE_REF" ] ; then
-              echo GITHUB_BASE_REF="master" >> $GITHUB_ENV     
+              export GITHUB_BASE_REF="master"
+              export GITHUB_BASE_REF="${GITHUB_BASE_REF}" >> $GITHUB_ENV     
           fi
+          echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT
   
       - name: Fetch commits through the merge base
         uses: BioData/fetch-through-merge-base@v0
         with:
-          base_ref: ${{ env.GITHUB_BASE_REF }}
+          base_ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
           head_ref: ${{ github.sha }}
 
       - name: set path

From 5fce79760b215a5b144564f1a0bafe35505e6620 Mon Sep 17 00:00:00 2001
From: Nils Homer <nh13@users.noreply.github.com>
Date: Tue, 21 Jan 2025 22:40:55 -0700
Subject: [PATCH 5/7] one more

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

diff --git a/.github/workflows/PR.yml b/.github/workflows/PR.yml
index 7ba7f607d6e47..829003765c6ee 100644
--- a/.github/workflows/PR.yml
+++ b/.github/workflows/PR.yml
@@ -172,13 +172,15 @@ jobs:
         id: github_base_ref
         run: |
           if [ -z "$GITHUB_BASE_REF" ] ; then
-              echo GITHUB_BASE_REF="master" >> $GITHUB_ENV     
+              export GITHUB_BASE_REF="master"
+              export GITHUB_BASE_REF="${GITHUB_BASE_REF}" >> $GITHUB_ENV     
           fi
+          echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT
   
       - name: Fetch commits through the merge base
         uses: BioData/fetch-through-merge-base@v0
         with:
-          base_ref: ${{ env.GITHUB_BASE_REF }}
+          base_ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
           head_ref: ${{ github.sha }}
 
       - name: set path

From 2cc8bd1a05dcfd41f776dbc252f4f284d83654eb Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Wed, 22 Jan 2025 14:07:27 +0000
Subject: [PATCH 6/7] Update snakemake-executor-plugin-slurm to 0.14.3

---
 recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml
index 171976c0ae9ef..020d76a469cb7 100644
--- a/recipes/snakemake-executor-plugin-slurm/meta.yaml
+++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "snakemake-executor-plugin-slurm" %}
-{% set version = "0.14.2" %}
+{% set version = "0.14.3" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz
-  sha256: c9a3266b7a53a9f32bcf995a5c59e35235703398abf8ca5393eed124723f1ed5
+  sha256: b1846d147fe6a2bf4f47aa35bc65ee99942f83aba7a9d41faf097bdbf5460807
 
 build:
   noarch: python

From 8e7af7b58037270ec9346b887134ab90604a371c Mon Sep 17 00:00:00 2001
From: Nils Homer <nh13@users.noreply.github.com>
Date: Wed, 22 Jan 2025 15:59:25 -0700
Subject: [PATCH 7/7] update action

---
 .github/workflows/PR.yml             | 18 +++++++++---------
 .github/workflows/build-failures.yml |  6 +++---
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/PR.yml b/.github/workflows/PR.yml
index 829003765c6ee..274767126f86c 100644
--- a/.github/workflows/PR.yml
+++ b/.github/workflows/PR.yml
@@ -25,10 +25,10 @@ jobs:
           echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT
   
       - name: Fetch commits through the merge base
-        uses: BioData/fetch-through-merge-base@v0
+        uses: fulcrumgenomics/fetch-through-merge-base@v1
         with:
-          base_ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
-          head_ref: ${{ github.sha }}
+          base-ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
+          head-ref: ${{ github.sha }}
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
@@ -81,10 +81,10 @@ jobs:
           echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT
   
       - name: Fetch commits through the merge base
-        uses: BioData/fetch-through-merge-base@v0
+        uses: fulcrumgenomics/fetch-through-merge-base@v1
         with:
-          base_ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
-          head_ref: ${{ github.sha }}
+          base-ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
+          head-ref: ${{ github.sha }}
 
 
       - name: set path
@@ -178,10 +178,10 @@ jobs:
           echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT
   
       - name: Fetch commits through the merge base
-        uses: BioData/fetch-through-merge-base@v0
+        uses: fulcrumgenomics/fetch-through-merge-base@v1
         with:
-          base_ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
-          head_ref: ${{ github.sha }}
+          base-ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
+          head-ref: ${{ github.sha }}
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
diff --git a/.github/workflows/build-failures.yml b/.github/workflows/build-failures.yml
index 4197cfee555a9..0c0654a02c1f2 100644
--- a/.github/workflows/build-failures.yml
+++ b/.github/workflows/build-failures.yml
@@ -28,10 +28,10 @@ jobs:
           echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT
   
       - name: Fetch commits through the merge base
-        uses: BioData/fetch-through-merge-base@v0
+        uses: fulcrumgenomics/fetch-through-merge-base@v1
         with:
-          base_ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
-          head_ref: ${{ github.sha }}
+          base-ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
+          head-ref: ${{ github.sha }}
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH