Benchmarks oct 23 fix

.github/workflows/benchmarks.yml

@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+
   pull_request_target:
     branches:
-      - '*'
+      - master
+
     types:
       - opened
       - reopened
@@ -38,10 +40,10 @@ jobs:
       - name: Checkout pull/${{ github.event.number }}
         uses: actions/checkout@v3
         with:
-          ref: ${{ github.event.pull_request.head.sha }}
+          ref: ${{ github.sha }}
           fetch-depth: 0
         if: github.event_name == 'pull_request_target'
-      
+
       - name: Restore Atom Data
         uses: actions/cache/restore@v3
         id: atom-data-restore
@@ -62,24 +64,34 @@ jobs:
         with:
           path: benchmarks/data/kurucz_cd23_chianti_H_He.h5
           key: atom-data
+
+      - name: Setup Mamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: benchmark
+          init-shell: >-
+            bash
+          create-args: >-
+            python
+            asv
+            mamba
 
       - name: Install asv
-        run: pip install asv==0.5.*
+        run: pip install asv
 
       - name: Accept all asv questions
         run: asv machine --yes
 
       - name: Run benchmarks for last 5 commits if not PR
         if: github.event_name != 'pull_request_target'
-        continue-on-error: true
         run: |
           git log -n 5  --pretty=format:"%H" >> tag_commits.txt
           asv run HASHFILE:tag_commits.txt | tee asv-output.log  
           if grep -q failed asv-output.log; then 
             echo "Some benchmarks have failed!"
             exit 1
           fi
-          
+
       - name: Generate Graphs and HTML
         if: github.event_name != 'pull_request_target'
         run: asv publish

.github/workflows/docstr-cov.yml

@@ -31,12 +31,12 @@ jobs:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.x
 
       - name: Install interrogate
-        run: pip install interrogate==1.5.0 parse==1.19.0
+        run: pip install interrogate==1.5.0 parse==1.19.0 setuptools
 
       - name: Get SHAs
         run: |

.github/workflows/pre-release.yml

@@ -15,36 +15,6 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  lock:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Setup environment
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-            miniforge-variant: Mambaforge
-            miniforge-version: latest
-            auto-activate-base: true
-            activate-environment: ""
-            use-mamba: true
-
-      - name: Install conda-lock
-        run: mamba install -c conda-forge conda-lock=1.0.5
-
-      - name: Generate lockfiles
-        run: |
-          conda-lock -f tardis_env3.yml -p linux-64 -p osx-64
-          conda lock render conda-lock.yml
-
-      - uses: actions/upload-artifact@v3
-        with:
-          name: lockfiles
-          path: |
-              conda-linux-64.lock
-              conda-osx-64.lock
-              conda-lock.yml
-
   zenodo:
     runs-on: ubuntu-latest
     steps:
@@ -58,6 +28,9 @@ jobs:
         env:
           KEY_SECRET_JSON: ${{ secrets.ZENODO_KEY_SECRET_JSON }}
 
+      - name: Download Lock File
+        run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
+
       - name: Setup environment
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -80,7 +53,7 @@ jobs:
           path: .zenodo.json
 
   pull_request:
-    needs: [lock, zenodo]
+    needs: zenodo
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
@@ -89,11 +62,8 @@ jobs:
         with:
           path: /tmp
 
-      - name: Copy files to repository
+      - name: Copy zenodo.json to repository
         run: |
-          cp /tmp/lockfiles/conda-linux-64.lock .
-          cp /tmp/lockfiles/conda-osx-64.lock .
-          cp /tmp/lockfiles/conda-lock.yml .
           cp /tmp/zenodo_json/.zenodo.json .
 
       - name: Get current date

.github/workflows/tests.yml

@@ -15,8 +15,8 @@ on:
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually
-  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata
-                --cov=tardis --cov-report=xml --cov-report=html
+  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --tardis-snapshot-data=${{ github.workspace }}/tardis-regressions
+                --cov=tardis --cov-report=xml --cov-report=html 
   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
 concurrency:
@@ -32,20 +32,22 @@ jobs:
     if: github.repository_owner == 'tardis-sn'
     strategy:
       matrix:
+        pip: [true, false]
+        label: [osx-64, linux-64]
         include:
+          - label: osx-64
+            os: macos-latest
+            prefix: /Users/runner/miniconda3/envs/tardis
 
-        - os: ubuntu-latest
-          label: linux-64
-          prefix: /usr/share/miniconda3/envs/tardis
+          - label: linux-64
+            os: ubuntu-latest
+            prefix: /usr/share/miniconda3/envs/tardis
 
-        - os: macos-latest
-          label: osx-64
-          prefix: /Users/runner/miniconda3/envs/tardis
-
-    name: ${{ matrix.label }}
+    name: ${{ matrix.label }}-pip-${{ matrix.pip }}
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v2
+        if: matrix.pip == false
 
       - name: Clone tardis-sn/tardis-refdata
         uses: actions/checkout@v2
@@ -84,6 +86,12 @@ jobs:
         with:
           path: tardis-refdata/.git/lfs
           key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v1
+
+      - name: Clone tardis-sn/tardis-regressions
+        uses: actions/checkout@v4
+        with:
+          repository: tardis-sn/tardis-regressions
+          path: tardis-regressions
 
       - name: Setup environment
         uses: conda-incubator/setup-miniconda@v2
@@ -93,6 +101,10 @@ jobs:
             activate-environment: tardis
             use-mamba: true
 
+      - name: Download Lock File
+        run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-${{ matrix.label }}.lock
+        if: matrix.pip == true
+
       - uses: actions/cache@v2
         with:
           path: ${{ matrix.prefix }}
@@ -102,12 +114,33 @@ jobs:
       - name: Update environment
         run: mamba update -n tardis --file conda-${{ matrix.label }}.lock
         if: steps.cache-conda.outputs.cache-hit != 'true'
-
-      - name: Install package
-        run: pip install -e .
+
+      - name: Install package editable
+        run: | 
+          pip install -e .
+          echo "TARDIS_PIP_PATH=tardis" >> $GITHUB_ENV
+        if: matrix.pip == false
+
+      - name: Install package git
+        run: pip install git+https://github.com/tardis-sn/tardis.git@${{ github.ref }}
+        if: matrix.pip == true
+
+      - name: Set pip path
+        if: matrix.pip == true
+        run: |
+          location_line=$(pip show tardis | grep -i -x "Location:.*")
+          directory_path=$(echo $location_line | awk -F " " '{print $2}')
+          echo "TARDIS_PIP_PATH=$directory_path" >> $GITHUB_ENV
+
+      - name: Set install path
+        if: matrix.pip == false
+        run: |
+          directory_path="."
+          echo "TARDIS_PIP_PATH=$directory_path" >> $GITHUB_ENV
 
       - name: Run tests
         run: pytest tardis ${{ env.PYTEST_FLAGS }}
+        working-directory: ${{ env.TARDIS_PIP_PATH }}
 
       - name: Upload to Codecov
         run: bash <(curl -s https://codecov.io/bash)

.mailmap

@@ -5,6 +5,7 @@ Alexander Holas <alexander.holas@h-its.org>
 Alexander Holas <alex.holas@gmx.de>
 Alexander Holas <alexander.holas@h-its.org> AlexHls <70367168+AlexHls@users.noreply.github.com>
 Alexander Holas <alexander.holas@h-its.org> AlexHls <alexander.holas@h-its.org>
+Alexander Holas <70367168+AlexHls@users.noreply.github.com>
 
 Alice Harpole <aliceharpole@gmail.com>
 Alice Harpole <aliceharpole@gmail.com> Alice Harpole <harpolea@users.noreply.github.com>
@@ -41,6 +42,8 @@ Atharwa Kharkar <atharwa.kharkar19@vit.edu> atharwa_24 <atharwa.kharkar19@vit.ed
 
 Atul Kumar <kr.atul.atk@gmail.com>
 
+Anirban Dutta <anirbaniamdutta@gmail.com>
+
 Barnabás Barna <bbarna@titan.physx.u-szeged.hu>
 
 Caroline Sofiatti <c.sofiatti@gmail.com>
@@ -102,6 +105,8 @@ John Reichenbach <56849859+jreichenbach-msu@users.noreply.github.com>
 Jordi Eguren <jordi.eguren.brown@gmail.com>
 Jordi Eguren <jordi.eguren.brown@gmail.com> jordi5 <45364266+jordi5@users.noreply.github.com>
 
+Josh Shields <shields.joshua.v@gmail.com>
+
 Karan Desai <karandesai_96@live.com>
 Karan Desai <karandesai_96@live.com> karandesai-96 <karandesai_96@live.com>