From 3d1e919b722f3bbf92b2713e5578be7ed9903e87 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 28 Sep 2023 09:04:37 +0200
Subject: [PATCH 1/5] use caching from setup-python

---
 .github/workflows/pytest.yml | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 109697960e..ea617e463b 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -42,18 +42,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-
-      - name: Cache python dependencies
-        uses: actions/cache@v3
-        id: pip_cache
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements-dev.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - if: ${{ steps.pip_cache.outputs.cache-hit != 'true' }}
-        name: Install python dependencies
+          cache: "pip"
         run: |
           python -m pip install --upgrade pip -r requirements-dev.txt
           pip install -e .

From 5ade7ec94e109343d98c555029ce738da4714ba8 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 28 Sep 2023 09:06:44 +0200
Subject: [PATCH 2/5] fix syntax

---
 .github/workflows/pytest.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index ea617e463b..34caa7b26d 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -43,6 +43,8 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
+
+      - name: Install dependencies
         run: |
           python -m pip install --upgrade pip -r requirements-dev.txt
           pip install -e .

From 83c71831ec76c48ac82ca0d23c54a020a2065528 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 28 Sep 2023 09:22:20 +0200
Subject: [PATCH 3/5] invalidate nextflow cache once per month

---
 .github/workflows/pytest.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 34caa7b26d..3ecdceedc5 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -43,7 +43,6 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
-
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip -r requirements-dev.txt
@@ -56,13 +55,17 @@ jobs:
           sudo apt remove git git-man
           sudo add-apt-repository --remove ppa:git-core/ppa
           sudo apt install git
+      - name: Get current date
+        id: date
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
       - name: Cache Nextflow
         uses: actions/cache@v3
         id: nfcore_cache
         with:
           path: ~/.nextflow
-          key: ${{ runner.os }}-nextflow-${{ hashFiles('nextflow.config') }}
+          # use date
+          key: ${{ runner.os }}-nextflow-${{ steps.date.outputs.date }}
           restore-keys: |
             ${{ runner.os }}-nextflow-
 

From 58b68cfa6f8c18a81ba890ce110e4cf04b0d5f15 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 28 Sep 2023 14:23:02 +0200
Subject: [PATCH 4/5] fix github token

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

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 3ecdceedc5..d343c3ed0b 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -21,7 +21,7 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  GITHUB_TOKEN: ${{ github.token }}
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
   pytest:

From c47932a6862dfacd9e34ba23e3e59861ed33dd83 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 28 Sep 2023 14:23:26 +0200
Subject: [PATCH 5/5] remove caching of nextflow step

---
 .github/workflows/pytest.yml | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index d343c3ed0b..388aaeb3d7 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -59,18 +59,7 @@ jobs:
         id: date
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
-      - name: Cache Nextflow
-        uses: actions/cache@v3
-        id: nfcore_cache
-        with:
-          path: ~/.nextflow
-          # use date
-          key: ${{ runner.os }}-nextflow-${{ steps.date.outputs.date }}
-          restore-keys: |
-            ${{ runner.os }}-nextflow-
-
-      - if: ${{ steps.nfcore_cache.outputs.cache-hit != 'true' }}
-        name: Install Nextflow
+      - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "latest-everything"