Features/updated notebooks

.github/workflows/notebooks.yml

@@ -0,0 +1,39 @@
+name: Test notebooks
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.11"  # Specify the Python version you need
+
+    - name: Install gfortran
+      run: |
+        sudo apt-get -y update
+        sudo apt-get -y install gfortran
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest nbmake pytest-xdist jupyter
+
+    - name: Install package in editable mode
+      run: |
+        pip install -e .
+
+    - name: Test notebooks
+      run: |
+        pytest -n auto --nbmake --nbmake-timeout=2400 --nbmake-kernel=python3 notebooks
+
+

.github/workflows/pytest.yml

@@ -1,4 +1,4 @@
-name: Run pytest
+name: Test install and interface
 
 on:
   pull_request:
@@ -27,13 +27,17 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest
+        pip install pytest pytest-xdist
 
     - name: Install package in editable mode
       run: |
         pip install -e .
 
-    - name: Run pytest
+    - name: Run pytest install test
       run: |
-        pytest tests/  # Specify the path to your 'tests' directory
+        pytest tests/test_install.py
+
+    - name: Run pytest install test
+      run: |
+        pytest -n auto tests/{test_ode_conservation.py,test_run_stages.py}
 

.gitignore

@@ -19,4 +19,5 @@ build
 dist
 */__pycache__
 .venv
-conda*
+conda*
+.conda

.pre-commit-config.yaml

@@ -0,0 +1,15 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.6.9
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+- repo: https://github.com/kynan/nbstripout
+  rev: 0.7.1
+  hooks:
+    - id: nbstripout
+

Makerates/comparenetworks.py

@@ -14,11 +14,15 @@
 
 print("\nReading reactions")
 reactions1, drops = read_reaction_file(reactionsFile1, speciesList, "UCL")
-print(f"I found {len(reactions1)} reactions in the file {reactionsFile1}, I dropped {len(drops)} reactions.")
+print(
+    f"I found {len(reactions1)} reactions in the file {reactionsFile1}, I dropped {len(drops)} reactions."
+)
 # If you need to see which reactions are dropped:
 # print("\n".join([str(drop) for drop in drops]))
 reactions2, drops = read_reaction_file(reactionsFile2, speciesList, "UCL")
-print(f"I found {len(reactions2)} reactions in the file {reactionsFile2}, I dropped {len(drops)} reactions.")
+print(
+    f"I found {len(reactions2)} reactions in the file {reactionsFile2}, I dropped {len(drops)} reactions."
+)
 
 
 print("\nReactions from file 1 not in file 2")

Makerates/speciesnetwork.py

@@ -1,20 +1,44 @@
-#simple python script that reads a Makerates produced reaction file and prints every reaction that forms or destroys a chosen species.
+# simple python script that reads a Makerates produced reaction file and prints every reaction that forms or destroys a chosen species.
 from __future__ import print_function
 import csv
 
-species='HCN'
+species = "HCN"
 
-f=open('outputFiles/reactions.csv')
-reader=csv.reader(f, delimiter=',', quotechar='|')
+f = open("outputFiles/reactions.csv")
+reader = csv.reader(f, delimiter=",", quotechar="|")
 
-forms='Species Formed in: \n'
-dest='Species Destroyed in: \n'
+forms = "Species Formed in: \n"
+dest = "Species Destroyed in: \n"
 for row in reader:
-	if len(row)>1:
-		if species in [row[0],row[1],row[2]]:
-			dest=dest+row[0]+' + '+row[1]+' --> '+row[3]+' + '+row[4]+' + '+row[5]+'\n'
-		elif species in [row[3],row[4],row[5]]:
-			forms=forms+row[0]+' + '+row[1]+' --> '+row[3]+' + '+row[4]+' + '+row[5]+'\n'
+    if len(row) > 1:
+        if species in [row[0], row[1], row[2]]:
+            dest = (
+                dest
+                + row[0]
+                + " + "
+                + row[1]
+                + " --> "
+                + row[3]
+                + " + "
+                + row[4]
+                + " + "
+                + row[5]
+                + "\n"
+            )
+        elif species in [row[3], row[4], row[5]]:
+            forms = (
+                forms
+                + row[0]
+                + " + "
+                + row[1]
+                + " --> "
+                + row[3]
+                + " + "
+                + row[4]
+                + " + "
+                + row[5]
+                + "\n"
+            )
 
 print(forms)
-print(dest)
+print(dest)