fix the RMG-Py conda build

changes required to make the RMG-Py conda build work again. detailed description: - recipe now contains the appropriate requirements - removed macos travis-specific thing - added comments in build.sh for historical preservation of my failed efforts - other changes are the initial steps toward making the conda build work, future commits will make the build tests pass the ci runs on a self-hosted runner in the green group offices. required a specific version of conda build and libmamba to be installed (see PR of this commit for more details), currently fails tests because rmg tries to import Julia during testing. will now need to 'bury' the Julia import and make it optional, including docs updates, etc.
ReactionMechanismGenerator · Sep 27, 2023 · af201e0 · af201e0
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diff --git a/.conda/build.sh b/.conda/build.sh
@@ -1,6 +1,15 @@
-# Install RMG
+# conda build script
+#
+# conda executes this script during the build process to make the rmg
+# binary
 make install
 
-# lazy "install" of everything in our 'external' folder.
-# most of which should probably be elsewhere
-cp -R ${SRC_DIR}/external ${SP_DIR}
+# The below code does not work because the Julia programming langauge is a very interesting technical demo that is completely unfit for actual
+# deployment in any real world projects.
+# 
+# RMG will be shipped as a pure python package, and then RMS installed by the user.
+#
+# export PYTHON=$PREFIX/bin/python
+# export PYTHONPATH=$SRC_DIR:$PYTHONPATH
+# python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
+# julia -e 'using Pkg; Pkg.add(PackageSpec(name="Functors",version="0.4.3")); Pkg.pin("Functors"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator'
diff --git a/.conda/conda_build_config.yaml b/.conda/conda_build_config.yaml
@@ -3,6 +3,3 @@ python:
 numpy:
   - 1.15
 
-# Specifically for Travis build. Should change if building locally.
-CONDA_BUILD_SYSROOT:
-  - /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk # [osx] 
diff --git a/.conda/meta.yaml b/.conda/meta.yaml
@@ -13,73 +13,174 @@ requirements:
   build:
     - {{ compiler('c') }}
   host:
+    - cairo
+    - cairocffi
+    - ffmpeg
+    - xlrd
+    - xlwt
+    - h5py
+    - graphviz
+    - markupsafe
+    - psutil
+    - ncurses
+    - suitesparse
+
+  # external software tools for chemistry
+    - coolprop
+    - cantera=2.6
+    - mopac
+    - cclib >=1.6.3,!=1.8.0
+    - openbabel >=3
+
+  # Python tools
+    - python >=3.7
+    - coverage
     - cython >=0.25.2
+    - scikit-learn
+    - scipy
+    - numpy >=1.10.0
+    - pydot
+    - jinja2
+    - jupyter
+    - pymongo
+    - pyparsing
+    - pyyaml
+    - networkx
+    - matplotlib >=1.5
+    - mpmath
+    - pandas
+
+  # packages we maintain
+    - rmgdatabase
+    - gprof2dot
     - lpsolve55
-    - numpy
-    - openbabel >=3
-    - pydas >=1.0.2
-    - pydqed >=1.0.1
+    - muq2
+    - numdifftools
+    - pydas >=1.0.3
+    - pydqed >=1.0.3
     - pyrdl
-    - python
     - quantities
-    - rdkit >=2018
-    - scipy
-    - setuptools
+    - symmetry
+    - chemprop==0.0.1
+    - rdkit >=2020.03.3.0
+
+    - liblapack =*=*mkl
   run:
     - cairo
     - cairocffi
-    - cantera >=2.3.0
-    - cclib >=1.6.3
-    - chemprop
+    - ffmpeg
+    - xlrd
+    - xlwt
+    - h5py
+    - graphviz
+    - markupsafe
+    - psutil
+    - ncurses
+    - suitesparse
+
+  # external software tools for chemistry
     - coolprop
+    - cantera=2.6
+    - mopac
+    - cclib >=1.6.3,!=1.8.0
+    - openbabel >=3
+
+  # Python tools
+    - python >=3.7
     - coverage
     - cython >=0.25.2
-    - ffmpeg
-    - gprof2dot
-    - graphviz
-    - h5py
+    - scikit-learn
+    - scipy
+    - numpy >=1.10.0
+    - pydot
     - jinja2
     - jupyter
-    - lpsolve55
-    - markupsafe
+    - pymongo
+    - pyparsing
+    - pyyaml
+    - networkx
     - matplotlib >=1.5
-    - mopac
     - mpmath
+    - pandas
+
+  # packages we maintain
+    - rmgdatabase
+    - gprof2dot
+    - lpsolve55
     - muq2
-    - networkx
-    - nose
     - numdifftools
-    - {{ pin_compatible('numpy') }}
-    - openbabel >=3
-    - pandas
+    - pydas >=1.0.3
+    - pydqed >=1.0.3
+    - pyrdl
+    - quantities
+    - symmetry
+    - chemprop==0.0.1
+    - rdkit >=2020.03.3.0
+
+    - liblapack =*=*mkl
+test:
+  requires:
+    - cairo
+    - cairocffi
+    - ffmpeg
+    - xlrd
+    - xlwt
+    - h5py
+    - graphviz
+    - markupsafe
     - psutil
-    - pydas >=1.0.2
+    - ncurses
+    - suitesparse
+
+  # external software tools for chemistry
+    - coolprop
+    - cantera=2.6
+    - mopac
+    - cclib >=1.6.3,!=1.8.0
+    - openbabel >=3
+
+  # Python tools
+    - python >=3.7
+    - coverage
+    - cython >=0.25.2
+    - scikit-learn
+    - scipy
+    - numpy >=1.10.0
     - pydot
-    - pydqed >=1.0.1
+    - jinja2
+    - jupyter
     - pymongo
     - pyparsing
-    - pyrdl
-    - python
     - pyyaml
-    - pyzmq
+    - networkx
+    - matplotlib >=1.5
+    - mpmath
+    - pandas
+
+  # packages we maintain
+    - rmgdatabase
+    - gprof2dot
+    - lpsolve55
+    - muq2
+    - numdifftools
+    - pydas >=1.0.3
+    - pydqed >=1.0.3
+    - pyrdl
     - quantities
-    - rdkit >=2018
-    - rmgdatabase >=3.2.0
-    - scikit-learn
-    - scipy
     - symmetry
-    - xlrd
-    - xlwt
-test:
+    - chemprop==0.0.1
+    - rdkit >=2020.03.3.0
+
+    - liblapack =*=*mkl
   source_files:
     - 'examples/rmg/superminimal'
     - 'examples/arkane/networks/n-butanol'
   imports:
     - rmgpy
     - arkane
   commands:
-    - python-jl rmg.py examples/rmg/superminimal/input.py
-    - python arkane.py examples/arkane/networks/n-butanol
+    - rmg.py examples/rmg/superminimal/input.py
+    - arkane.py examples/arkane/networks/n-butanol
 
 about:
   home: https://github.com/ReactionMechanismGenerator/RMG-Py

diff --git a/environment.yml b/environment.yml
@@ -45,10 +45,6 @@ dependencies:
   - conda-forge::cclib >=1.6.3,!=1.8.0
   - conda-forge::openbabel >= 3
 
-# general-purpose external software tools
-  - conda-forge::julia>=1.8.5,!=1.9.0
-  - conda-forge::pyjulia >=0.6
-
 # Python tools
   - python >=3.7
   - coverage
@@ -75,21 +71,20 @@ dependencies:
   - matplotlib >=1.5
   - mpmath
   - pandas
+  - conda-forge::numdifftools
 
 # packages we maintain
   - rmg::gprof2dot
   - rmg::lpsolve55
   - rmg::muq2
-  - rmg::numdifftools
   - rmg::pydas >=1.0.3
   - rmg::pydqed >=1.0.3
   - rmg::pyrdl
-  - rmg::pyrms
   - rmg::quantities
   - rmg::symmetry
 
 # packages we would like to stop maintaining (and why)
-  - rmg::diffeqpy
+  #- rmg::diffeqpy
   # we should use the official verison https://github.com/SciML/diffeqpy),
   # rather than ours (which is only made so that we can get it from conda)
   # It is only on pip, so we will need to do something like:
@@ -103,8 +98,7 @@ dependencies:
   # We should use the official channel, not sure how difficult this
   # change will be.
 
-# conda mutex metapackage
-  - nomkl
+  - liblapack =*=*mkl
 
 # additional packages that are required, but not specified here (and why)
   # pydqed, pydas, mopac, and likely others require a fortran compiler (specifically gfortran)

diff --git a/rmg.py b/rmg.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python-jl
+#!/usr/bin/env python
 
 ###############################################################################
 #                                                                             #

diff --git a/setup.py b/setup.py
@@ -215,7 +215,6 @@
     'scripts/standardizeModelSpeciesNames.py',
     'scripts/thermoEstimator.py',
     'scripts/isotopes.py',
-    'testing/databaseTest.py',
 ]
 
 modules = []

diff --git a/utilities.py b/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 python-jl
+    shebang = """#!/usr/bin/env python
 
 """