Updating Conda environment requirements

.github/workflows/CI.yml

@@ -94,7 +94,6 @@ jobs:
         run: |
           python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" || true
           julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' || true 
-          ln -sfn $(which python-jl) $(which python)
 
       # non-regression testing
       - name: Unit tests

.github/workflows/docs.yml

@@ -36,7 +36,6 @@ jobs:
           julia -e "using Pkg; Pkg.add(PackageSpec(url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl\", rev=\"main\"))"
           julia -e "using Pkg; Pkg.add(\"PyCall\"); Pkg.add(\"DifferentialEquations\")"
           python -c "import julia; julia.install()"
-          ln -sfn $(which python-jl) $(which python)
       - name: Install and compile RMG
         run: |
           cd ..

Dockerfile

@@ -56,7 +56,6 @@ RUN make
 # Install and link Julia dependencies for RMS
 RUN python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" || true
 RUN julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' || true 
-RUN ln -sfn $(which python-jl) $(which python)
 
 # RMG-Py should now be installed and ready
 RUN python-jl rmg.py --help

documentation/source/users/rmg/installation/anacondaDeveloper.rst

@@ -141,6 +141,77 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 You may now use RMG-Py, Arkane, as well as any of the :ref:`Standalone Modules <modules>` included in the RMG-Py package.
 
 
+Debugging
+=========
+
+If you wish to debug using the (very helpful) debugger in `VSCode <https://code.visualstudio.com>`_,
+here is an example launch configuration to put in your launch.json file,
+which can be found in the .vscode folder.
+You might have to edit them slightly to match your exact paths. Specifically, 
+you will need ``/opt/miniconda3/envs/rmg_env`` to point to where your conda environment is located.
+
+This configuration will allow you to debug the rms_constant_V example, running through
+python-jl. ::
+
+        {
+            "name": "Python: rmg.py rms_constant_V",
+            "type": "python",
+            "request": "launch",
+            "cwd": "${workspaceFolder}/",
+            "program": "rmg.py",
+            "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl",
+            "args": [
+                "examples/rmg/rms_constant_V/input.py",
+            ],
+            "console": "integratedTerminal",
+            "env": {
+                "PATH": "/opt/miniconda3/envs/rmg_env/bin:${env:PATH}",
+                "PYTHONPATH": "${workspaceFolder}/",
+            }
+        },
+
+This configuration will allow you to debug a subset of the unit tests.
+Open one of the many test files named `*Test.py` before you launch it::
+
+            {
+            "name": "Python: nosetest Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "/opt/miniconda3/envs/rmg_env/bin/nosetests",
+            "args": [
+                "--nologcapture",
+                "--nocapture",
+                "--verbose",
+                "${file}"
+            ],
+            "console": "integratedTerminal",
+            "env": {
+                "PATH": "/opt/miniconda3/envs/rmg_env/bin:${env:PATH}",
+                "PYTHONPATH": "${workspaceFolder}/",
+            },
+        },
+
+This configuration will allow you to debug running all the database tests.::
+
+        {
+            "name": "Test RMG-database",
+            "type": "python",
+            "request": "launch",
+            "program": "/opt/miniconda3/envs/rmg_env/bin/nosetests",
+            "args": [
+                "--nologcapture",
+                "--nocapture",
+                "--verbose",
+                "--detailed-errors",
+                "${workspaceFolder}/testing/databaseTest.py"
+            ],
+            "console": "integratedTerminal",
+            "env": {
+                "PATH": "/opt/miniconda3/envs/rmg_env/bin:${env:PATH}",
+                "PYTHONPATH": "${workspaceFolder}/",
+            },
+        },
+
 Test Suite
 ==========
 
@@ -188,3 +259,15 @@ A number of basic examples can be run immediately.  Additional example input fil
 
     cd RMG-Py
     make eg4
+
+
+Building Documentation
+======================
+To build the documentation (to test that you have it right before pushing to GitHub) you will need to install sphinx::
+
+    conda activate rmg_env
+    conda install sphinx
+
+Then you can build the documentation::
+
+    make documentation

documentation/source/users/rmg/running.rst

@@ -10,7 +10,7 @@ Running a basic RMG job is straightforward, as shown in the example below. Howev
 
 Basic run::
 
-	python rmg.py input.py
+	python-jl rmg.py input.py
 
 .. _inputflags:
 
@@ -19,7 +19,7 @@ Input flags
 
 The options for input flags can be found in ``/RMG-Py/rmgpy/util.py``. Running ::
 
- 	python rmg.py -h
+ 	python-jl rmg.py -h
 
 at the command line will print the documentation from ``util.py``, which is reproduced below for convenience::
 
@@ -63,23 +63,23 @@ Some representative example usages are shown below.
 
 Run by restarting from a seed mechanism::
 
-    python rmg.py -r path/to/seed/ input.py
+    python-jl rmg.py -r path/to/seed/ input.py
 
 Run with CPU time profiling::
 
-    python rmg.py -p input.py
+    python-jl rmg.py -p input.py
 
 Run with multiprocessing for reaction generation and QMTP::
 
-    python rmg.py -n <Max number of processes allowed> input.py 
+    python-jl rmg.py -n <Max number of processes allowed> input.py 
 
 Run with setting a limit on the maximum execution time::
 
-	python rmg.py -t <DD:HH:MM:SS> input.py
+	python-jl rmg.py -t <DD:HH:MM:SS> input.py
 
 Run with setting a limit on the maximum number of iterations::
 
-	python rmg.py -i <Max number of desired iterations> input.py
+	python-jl rmg.py -i <Max number of desired iterations> input.py
 
 
 Details on the multiprocessing implementation

environment.yml

@@ -47,6 +47,7 @@ dependencies:
 
 # general-purpose external software tools
   - conda-forge::julia>=1.8.5
+  - conda-forge::pyjulia >=0.6
 
 # Python tools
   - python >=3.7
@@ -94,16 +95,6 @@ dependencies:
   # We should use the official channel, not sure how difficult this
   # change will be.
 
-  - rmg::pyjulia
-  # This is identical to the conda-forge package, except that we run
-  # a hard to decipher sed command during the build process:
-  # https://github.com/ReactionMechanismGenerator/conda-recipes/blob/rmg-deps/pyjulia/build.sh#LL15C69-L15C69
-  #
-  # We should either remove the need to use this command or add this
-  # to the installation steps
-  # 
-  # Both pyrms and diffeqpy depend on this package.
-
 # conda mutex metapackage
   - nomkl
 

utilities.py

@@ -310,7 +310,7 @@ def update_headers():
     start of each file, be sure to double-check the results to make sure
     important lines aren't accidentally overwritten.
     """
-    shebang = """#!/usr/bin/env python3
+    shebang = """#!/usr/bin/env python-jl
 
 """