Move PR CI tests to Github Actions

.github/workflows/pr_tests.yml

@@ -0,0 +1,73 @@
+# Modified from GitHub Actions template
+
+name: Workflow
+
+# Improves reproducibility and speed
+env:
+  OPENBLAS_NUM_THREADS: 1
+  OMP_NUM_THREADS: 1
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  Reproducibility:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip wheel
+        pip install numpy==1.26.4
+        pip install -r requirements.txt
+    - name: Compile Cython components
+      run: |
+        make clean compile
+    - name: Test ParCa reproducibility
+      run: |
+        python runscript/parca.py -c 3 -o out/parca_1
+        python runscript/parca.py -c 3 -o out/parca_2
+        python runscript/debug/compare_pickles.py out/parca_1/kb out/parca_2/kb
+    - name: Test simulation reproducibility
+      run: |
+        python ecoli/experiments/ecoli_master_sim.py \
+            --generations 1 --no_suffix_time --emitter parquet --emitter_arg out_dir='out' \
+            --experiment_id "parca_1" --daughter_outdir "out/parca_1" \
+            --sim_data_path "out/parca_1/kb/simData.cPickle" --fail_at_total_time &
+        python ecoli/experiments/ecoli_master_sim.py \
+            --generations 1 --no_suffix_time --emitter parquet --emitter_arg out_dir='out' \
+            --experiment_id "parca_2" --daughter_outdir "out/parca_2" \
+            --sim_data_path "out/parca_2/kb/simData.cPickle" --fail_at_total_time && fg
+        python runscripts/debug/diff_simouts.py -o "out" "parca_1" "parca_2"
+  2 Gens:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip wheel
+        pip install numpy==1.26.4 mypy
+        pip install -r requirements.txt
+    - name: Compile Cython components
+      run: |
+        make clean compile
+    - name: Two generations
+      run: |
+      python runscripts/workflow.py --config ecoli/composites/ecoli_configs/test_installation.json

ecoli/composites/ecoli_configs/test_installation.json

@@ -4,7 +4,7 @@
     "parca_options": {
         "cpus": 1
     },
-    "generations": 1,
+    "generations": 2,
     "n_init_sims": 1,
     "single_daughters": true,
     "emitter" : {

ecoli/experiments/ecoli_master_sim.py

@@ -203,6 +203,12 @@ def __init__(
                     "in the configuration file."
                 ),
             )
+            self.parser.add_argument(
+                "--no_suffix_time",
+                action="store",
+                help=r"Do not append current time as'%d-%m-%Y_%H-%M-%S'"
+                    " to experiment ID.",
+            )
             self.parser.add_argument(
                 "--emitter",
                 action="store",

runscripts/jenkins/configs/ecoli-anaerobic.json

@@ -13,9 +13,7 @@
     "mass_distribution": false,
     "emitter" : {
         "type": "parquet",
-        "config": {
-            "out_dir": "/scratch/groups/mcovert/vecoli"
-        }
+        "out_dir": "/scratch/groups/mcovert/vecoli"
     },
     "analysis_options": {
         "single": {"mass_fraction_summary": {}}

runscripts/jenkins/configs/ecoli-glucose-minimal.json

@@ -5,9 +5,7 @@
     "fail_at_total_time": true,
     "emitter" : {
         "type": "parquet",
-        "config": {
-            "out_dir": "/scratch/groups/mcovert/vecoli"
-        }
+        "out_dir": "/scratch/groups/mcovert/vecoli"
     },
     "analysis_options": {
         "single": {"mass_fraction_summary": {}}

runscripts/jenkins/configs/ecoli-new-gene-gfp.json

@@ -5,9 +5,7 @@
     "fail_at_total_time": true,
     "emitter" : {
         "type": "parquet",
-        "config": {
-            "out_dir": "/scratch/groups/mcovert/vecoli"
-        }
+        "out_dir": "/scratch/groups/mcovert/vecoli"
     },
     "parca_options": {
         "new_genes": "gfp"

runscripts/jenkins/configs/ecoli-no-growth-rate-control.json

@@ -12,9 +12,7 @@
     "mechanistic_replisome": true,
     "emitter" : {
         "type": "parquet",
-        "config": {
-            "out_dir": "/scratch/groups/mcovert/vecoli"
-        }
+        "out_dir": "/scratch/groups/mcovert/vecoli"
     },
     "analysis_options": {
         "single": {"mass_fraction_summary": {}}

runscripts/jenkins/configs/ecoli-no-operons.json

@@ -5,9 +5,7 @@
     "fail_at_total_time": true,
     "emitter" : {
         "type": "parquet",
-        "config": {
-            "out_dir": "/scratch/groups/mcovert/vecoli"
-        }
+        "out_dir": "/scratch/groups/mcovert/vecoli"
     },
     "parca_options": {
         "operons": false

runscripts/jenkins/configs/ecoli-superhelical-density.json

@@ -6,9 +6,7 @@
     "superhelical_density": true,
     "emitter" : {
         "type": "parquet",
-        "config": {
-            "out_dir": "/scratch/groups/mcovert/vecoli"
-        }
+        "out_dir": "/scratch/groups/mcovert/vecoli"
     },
     "analysis_options": {
         "single": {"mass_fraction_summary": {}}

runscripts/jenkins/configs/ecoli-with-aa.json

@@ -5,9 +5,7 @@
     "fail_at_total_time": true,
     "emitter" : {
         "type": "parquet",
-        "config": {
-            "out_dir": "/scratch/groups/mcovert/vecoli"
-        }
+        "out_dir": "/scratch/groups/mcovert/vecoli"
     },
     "analysis_options": {
         "single": {"mass_fraction_summary": {}}