From 3cb08d756a416d8897adebe0b402eb52533ba504 Mon Sep 17 00:00:00 2001
From: WardDeb <ward@deboutte.be>
Date: Wed, 25 Sep 2024 13:42:24 +0200
Subject: [PATCH] tests via pip, drop conda

---
 .github/test_and_build.yml    | 20 -------------------
 .github/workflows/planemo.yml | 12 ------------
 .github/workflows/test.yml    | 37 ++++++++++++++---------------------
 3 files changed, 15 insertions(+), 54 deletions(-)
 delete mode 100644 .github/test_and_build.yml

diff --git a/.github/test_and_build.yml b/.github/test_and_build.yml
deleted file mode 100644
index 0d1c77b2..00000000
--- a/.github/test_and_build.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - python > 3.7
-  - numpy
-  - scipy
-  - flake8
-  - pysam
-  - deeptoolsintervals
-  - pytest
-  - samtools
-  - py2bit
-  - pyBigWig
-  - twine
-  - pip
-  - tomli  # remove dependency when lowest supported version is py 3.11
-  - pip:
-    - build
-    - planemo
\ No newline at end of file
diff --git a/.github/workflows/planemo.yml b/.github/workflows/planemo.yml
index 72a7bfe0..40d09cb5 100644
--- a/.github/workflows/planemo.yml
+++ b/.github/workflows/planemo.yml
@@ -39,22 +39,10 @@ jobs:
     name: Combine chunked test results
     needs: planemo_test
     runs-on: ubuntu-latest
-    # strategy:
-    #   matrix:
-    #     python-version: ['3.8', '3.11']
     steps:
     - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    # - uses: actions/setup-python@v5
-    #   with:
-    #     python-version: ${{ matrix.python-version }}
-    # - name: Cache .cache/pip
-    #   uses: actions/cache@v3
-    #   id: cache-pip
-    #   with:
-    #     path: ~/.cache/pip
-    #     key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ env.GALAXY_BRANCH }}
     - name: Combine outputs
       uses: galaxyproject/planemo-ci-action@v1
       id: combine
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 07ffd664..ff6687c4 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.base_ref == 'master'
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Check path
       run: find /home/runner/work/deepTools/deepTools -name "pyproject.toml"
     - name: Get Version of Deeptools
@@ -40,30 +40,26 @@ jobs:
     name: Test on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: mamba-org/setup-micromamba@main
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
-        environment-file: .github/test_and_build.yml
-        cache-downloads: true
-        environment-name: test_and_build
+        python-version: '3.12'
+        cache: 'pip'
     - name: pip install
       run: |
-        micromamba activate test_and_build
-        pip install .
+        pip install .[actions]
     - name: PEP8
       run: |
         micromamba activate test_and_build
         flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E722,W504,W605
     - name: Test deepTools
       run: |
-        micromamba activate test_and_build
         pytest -v
     - name: make an artifact
       run: |
-        micromamba activate test_and_build
         rm -f dist/*
         python -m build
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: "distfiles"
         path: "dist"
@@ -75,12 +71,12 @@ jobs:
       matrix:
         python-version: ['3.8','3.9','3.10', '3.11', '3.12']
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/download-artifact@v3
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
         with:
           name: "distfiles"
           path: ~/dist/
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
@@ -96,17 +92,14 @@ jobs:
     name: Test on OSX
     runs-on: macOS-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: mamba-org/setup-micromamba@main
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
-        environment-file: .github/test_and_build.yml
-        cache-downloads: true
-        environment-name: test_and_build
+        python-version: '3.12'
+        cache: 'pip'
     - name: pip install
       run: |
-        micromamba activate test_and_build
-        pip install .
+        pip install .[actions]
     - name: Test deepTools
       run: |
-        micromamba activate test_and_build
         pytest -v