From 0ef514fc20cdf8bc5382fe8f41d02c103ee9963d Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 4 Mar 2024 17:10:32 +0200
Subject: [PATCH] make compatible with master

---
 .github/workflows/test_and_publish.yml | 124 ++++++++++++-------------
 1 file changed, 62 insertions(+), 62 deletions(-)

diff --git a/.github/workflows/test_and_publish.yml b/.github/workflows/test_and_publish.yml
index 10959426e..21053653c 100644
--- a/.github/workflows/test_and_publish.yml
+++ b/.github/workflows/test_and_publish.yml
@@ -3,68 +3,68 @@ name: Test and deploy code
 on: [push]
 
 jobs:
-  # test:
-  #   runs-on: ${{ matrix.os }}
-
-  #   strategy:
-  #     fail-fast: false
-  #     matrix:
-  #       os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-  #       python-version: ["3.8", "3.9", "3.10"]
-
-  #   defaults: # Needed for conda
-  #     run:
-  #       shell: bash -l {0}
-
-  #   steps:
-  #     - uses: actions/checkout@v4
-  #       with:
-  #         lfs: true
-  #         submodules: true
-
-  #     - uses: conda-incubator/setup-miniconda@v3
-  #       with:
-  #         auto-update-conda: true
-  #         python-version: ${{ matrix.python-version }}
-  #         mamba-version: "*"
-  #         miniforge-variant: Mambaforge
-  #         channels: acellera,conda-forge,defaults
-
-  #     - name: Install Linux HTMD conda deps
-  #       if: matrix.os == 'ubuntu-latest'
-  #       run: |
-  #         mamba install --file package/htmd/DEPENDENCIES python=${{ matrix.python-version }} -y
-
-  #     - name: Install MacOS HTMD conda deps
-  #       if: matrix.os == 'macos-latest'
-  #       run: |
-  #         mamba install --file package/htmd/DEPENDENCIES_MAC python=${{ matrix.python-version }} -y
-
-  #     - name: Install Windows HTMD conda deps
-  #       if: matrix.os == 'windows-latest'
-  #       run: |
-  #         mamba install --file package/htmd/DEPENDENCIES_WIN python=${{ matrix.python-version }} -y
-
-  #     - name: Install pip dependencies
-  #       run: |
-  #         pip install flake8 pytest
-  #         pip install .
-
-  #     - name: Lint with flake8
-  #       run: |
-  #         # stop the build if there are Python syntax errors or undefined names
-  #         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-  #         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-  #         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-  #     - name: Test
-  #       run: |
-  #         export HTMD_NONINTERACTIVE=1
-  #         pytest --verbose --durations=10 ./htmd/
+  test:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    defaults: # Needed for conda
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          lfs: true
+          submodules: true
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          mamba-version: "*"
+          miniforge-variant: Mambaforge
+          channels: acellera,conda-forge,defaults
+
+      - name: Install Linux HTMD conda deps
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          mamba install --file package/htmd/DEPENDENCIES python=${{ matrix.python-version }} -y
+
+      - name: Install MacOS HTMD conda deps
+        if: matrix.os == 'macos-latest'
+        run: |
+          mamba install --file package/htmd/DEPENDENCIES_MAC python=${{ matrix.python-version }} -y
+
+      - name: Install Windows HTMD conda deps
+        if: matrix.os == 'windows-latest'
+        run: |
+          mamba install --file package/htmd/DEPENDENCIES_WIN python=${{ matrix.python-version }} -y
+
+      - name: Install pip dependencies
+        run: |
+          pip install flake8 pytest
+          pip install .
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Test
+        run: |
+          export HTMD_NONINTERACTIVE=1
+          pytest --verbose --durations=10 ./htmd/
 
   deploy:
-    # if: startsWith(github.event.ref, 'refs/tags/')
-    # needs: test
+    if: startsWith(github.event.ref, 'refs/tags/')
+    needs: test
     runs-on: ${{ matrix.os }}
     defaults: # Needed for conda
       run:
@@ -73,8 +73,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["windows-latest"]
-        python-version: ["3.8", "3.10"]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.8", "3.9", "3.10"]
 
     steps:
       - uses: actions/checkout@v4