Merge pull request #77 from uclchem/develop

We release UCLCHEM 3.4.0 with some additions to both user experience, technical improvements and new features:

    The biggest addition is a new mode where you can run UCLCHEM solely in memory, not requiring you to save and load the csv files that we relied on for long. A tutorial on how to do this, can be found in notebooks/2a_modelling_objects_on_disk.py
    We implement a new postprocessing mode, similar to what the NEATH paper does (https://fpriestley.github.io/neath/). This also allows for running much more flexible models.
    We now check whether the user specified branching ratios correctly, this means that if the total for reactions is larger than 1.0, we divide by the total. We also do it for three way split reactions, since often people write 0.33, resulting in 1% not being accounted for.
    We move to the RATE22 database as the default one, some species are renamed (https://umistdatabase.uk/)
    The tutorial notebooks have been moved to the notebooks directory and were revised a bit.
    radfield is now always a column in the output csv files, removing the need for two extra lines at the top of each uclchem csv file.
    A small chemistry network is added, this runs quickly and can be used for toy problems and code testing.

Small changes:

    The standard uv yield is now 0.03
    The magnetic field is now a parameter that can be passed for shock models
    The analysis scripts work once again in the gas phase, the grains still have some issues (see: 

Incorrect production and destruction in analysis.py #37)
We improved test coverage
We now have precommit configured to improve code quality

.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

@@ -18,3 +18,6 @@ test
 build
 dist
 */__pycache__
+.venv
+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/data/databases/dropped_from_umist22.csv

@@ -0,0 +1,3 @@
+# This file contains all the reactions we dropped from UMIST2, and the reasons why we dropped them!
+# Dropped because it conflicts with the default H2 Photodiss mechanism in UCLCHEM.
+8268:PH:H2:PHOTON:H:H:::1:5.70e-11:0.00:4.18:10:41000:C:C:"10.1051/0004-6361/201628742":"Heays, et al. A&A, 602, A105 (2017)":                                                                                                                                                                                  

Makerates/inputFiles/default_grain_network.csv → Makerates/data/default/default_grain_network.csv

@@ -26,7 +26,7 @@ H2,PHOTON,,H,H,,,1,1,0,,,
 #H2CO,CRP,,#HCO,#H,,,1.73E-14,0,0,,
 #H2CO,CRP,,#CO,H2,,,1.73E-14,0,0,,
 #CH3OH,CRP,,#CH2OH,#H,,,6.5E-15,0,0,,
-#CH3OH,CRP,,#H3CO,#H,,,6.5E-15,0,0,,
+#CH3OH,CRP,,#H2COH,#H,,,6.5E-15,0,0,,
 #CH3OH,CRP,,#CH3,#OH,,,1.95E-14,0,0,,
 #H2S,CRP,,#HS,H,,,3E-16,0,0,,
 #HCOOH,CRP,,#HCOO,H,,,3E-16,0,0,,
@@ -66,10 +66,10 @@ H2,PHOTON,,H,H,,,1,1,0,,,
 #H,#HCO,LH,#H2CO,,,,0.5,0,0,,,
 #H,#HCO,LH,#CO,#H2,,,0.5,0,0,,,
 #H,#H2CO,LH,#CH2OH,,,,0.33,0,5400,,,
-#H,#H2CO,LH,#H3CO,,,,0.33,0,2200,,,
+#H,#H2CO,LH,#H2COH,,,,0.33,0,2200,,,
 #H,#H2CO,LH,#HCO,#H2,,,0.33,0,1740,,,
 #H,#CH2OH,LH,#CH3OH,,,,1,0,0,,,
-#H,#H3CO,LH,#CH3OH,,,,1,0,0,,,
+#H,#H2COH,LH,#CH3OH,,,,1,0,0,,,
 #SI,#H,LH,#SIH,,,,1.0,0,0,,,
 #SIH,#H,LH,#SIH2,,,,1.0,0,0,,,
 #SIH2,#H,LH,#SIH3,,,,1.0,0,0,,,
@@ -118,7 +118,7 @@ HOCN,H,,HNCO,H,,,1.0E-10,0,2000,,,
 HONC,H,,HCNO,H,,,1.0E-10,0,2000,,,
 !
 #NH,#CO,LH,#HNCO,,,,1,0,4200,,, 
-#H3CO,#HNCO,LH,#CH3OH,#OCN,,,0,0,1200,,,
+#H2COH,#HNCO,LH,#CH3OH,#OCN,,,0,0,1200,,,
 #CH3,#HNCO,LH,#CH4,#OCN,,,0,0,1200,,,
 #NH,#HNCO,LH,#NH2,#OCN,,,0,0,1200,,,
 #NH2,#HNCO,LH,#NH3,#OCN,,,0,0,1200,,,
@@ -145,13 +145,13 @@ HONC,H,,HCNO,H,,,1.0E-10,0,2000,,,
 #NH2,#H2CO,LH,#NH2CHO,H,,,0.5,0,0,,,
 #NH2,#H2CO,LH,#NH3,#HCO,,,0.5,0,0,,,
 H,#H2NCO,LH,#HNCO,H2,,,1.0,0,0,,,! NOBLE ET AL. 2015
-NH2,H2CO,,NH2CHO,H,,,77.9E-16,-2.56,25,,,! SKOUTERIS ET AL. 2017
+! NH2,H2CO,,NH2CHO,H,,,77.9E-16,-2.56,25,,,! SKOUTERIS ET AL. 2017
 !
 ! (GARROD 2006)
 !
-#HCO,#H3CO,LH,#HCOOCH3,,,,1.0,0,0,,,
+#HCO,#H2COH,LH,#HCOOCH3,,,,1.0,0,0,,,
 #HCO,#CH2OH,LH,#HCOOCH3,,,,1.0,0,0,,,
-#CH3,#H3CO,LH,#CH3OCH3,,,,1.0,0,0,,,
+#CH3,#H2COH,LH,#CH3OCH3,,,,1.0,0,0,,,
 #HCO,#OH,LH,#HCOOH,,,,1.0,0,0,,,
 #CH3,#C2H3,LH,#CH3CHCH2,,,,1.0,0,0,,,
 #CH3,#HCO,LH,#CH3CHO,,,,1.0,0,0,,,
@@ -165,7 +165,7 @@ NH2,H2CO,,NH2CHO,H,,,77.9E-16,-2.56,25,,,! SKOUTERIS ET AL. 2017
 C3H5+,FREEZE,,#CH3CCH,H,,,1,1,0,,,
 CH3OH2+,FREEZE,,#CH3OH,H,,,1,1,0,,,
 C2N2+,FREEZE,,#NCCN,,,,1,0,0,,,
-HSIS+,FREEZE,,#SIS,H,,,1,1,0,,,
+SISH+,FREEZE,,#SIS,H,,,1,1,0,,,
 SIH5+,FREEZE,,#SIH4,H,,,1,1,0,,,
 H2CL+,FREEZE,,#HCL,H,,,1,1,0,,,
 !COOCH4+,FREEZE,,#HCOOCH3,,,,1,1,0,,,
@@ -174,15 +174,15 @@ HCO2+,FREEZE,,#CO2,H,,,1,1,0,,,
 CH5+,FREEZE,,#CH4,H,,,1,1,0,,,
 H2NO+,FREEZE,,#HNO,H,,,1,1,0,,,
 H3S+,FREEZE,,#H2S,H,,,1,1,0,,,
-H3CS+,FREEZE,,#H2CS,H,,,1,1,0,,,
+H2CSH+,FREEZE,,#H2CS,H,,,1,1,0,,,
 HSO+,FREEZE,,#SO,H,,,1,1,0,,,
-HOCS+,FREEZE,,#OCS,H,,,1,1,0,,,
+OCSH+,FREEZE,,#OCS,H,,,1,1,0,,,
 NH4+,FREEZE,,#NH3,H,,,1,1,0,,,
 HCNH+,FREEZE,,#HCN,H,,,1,1,0,,,
 N2H+,FREEZE,,#N2,H,,,1,1,0,,,
 HNS+,FREEZE,,#NS,H,,,1,1,0,,,
 C3+,FREEZE,,#C2,C,,,1,1,0,,,
-HSO2+,FREEZE,,#SO2,H,,,1,1,0,,,
+HOSO+,FREEZE,,#SO2,H,,,1,1,0,,,
 SIOH+,FREEZE,,#HSIO,,,,1,1,0,,,
 #HSIO,DESORB,,SIOH+,,,,1,1,0,,,
 HOC+,FREEZE,,#HCO,,,,1.0,1,0,,,