build an rmgmolecule package in place, fix conda builds

 - small updates to rmg-py recipe
 - removed conda_build.yml action since it will now be done in a private repo
 - added a recipe for rmgmolecule
 - add warnings on molecule when running from rmgmolecule that some functionality is not available

Author: JacksonBurns

.conda/meta.yaml

@@ -11,7 +11,7 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }} # [unix]
+    - {{ compiler('c') }}
   host:
     - cython >=0.25.2
     - lpsolve55
@@ -78,10 +78,8 @@ test:
     - rmgpy
     - arkane
   commands:
-    - rmg.py examples/rmg/superminimal/input.py # [unix]
-    - Arkane.py examples/arkane/networks/n-butanol/input.py # [unix]
-    - python %SCRIPTS%\rmg.py examples\rmg\superminimal\input.py # [win]
-    - python %SCRIPTS\Arkane.py examples\arkane\networks\n-butanol\input.py # [win]
+    - python-jl rmg.py examples/rmg/superminimal/input.py
+    - python arkane.py examples/arkane/networks/n-butanol
 
 about:
   home: https://github.com/ReactionMechanismGenerator/RMG-Py

.github/workflows/conda_build.yml

@@ -0,0 +1,2 @@
+# Install rmgmolecule
+python rmgmolecule_setup.py install

.rmgmolecule_conda/build.sh

@@ -0,0 +1,2 @@
+numpy:
+  - 1.19

.rmgmolecule_conda/conda_build_config.yaml

@@ -0,0 +1,53 @@
+# meta.yaml - package specification for rmgmolecule subpackage
+package:
+  name: rmgmolecule
+  version: 1.0.0
+
+source:
+  path: ../
+
+build:
+  number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
+
+requirements:
+  build:
+    - {{ compiler('c') }} # [unix]
+  host:
+    - cython >=0.25.2
+    - lpsolve55
+    - numpy
+    - openbabel >=3
+    - pyrdl
+    - python==3.7
+    - quantities
+    - rdkit >=2018
+    - scipy
+    - scikit-learn
+    - setuptools
+  run:
+    - cairo
+    - cairocffi
+    - cython >=0.25.2
+    - gprof2dot
+    - graphviz
+    - jinja2
+    - jupyter
+    - lpsolve55
+    - {{ pin_compatible('numpy') }}
+    - openbabel >=3
+    - pydot
+    - pyrdl
+    - python==3.7
+    - quantities
+    - rdkit >=2018
+    - scikit-learn
+test:
+  imports:
+    - rmgpy.molecule
+  commands:
+    - python -c 'from rmgpy.molecule import Molecule; mol=Molecule().from_smiles("CC")'
+
+about:
+  home: https://github.com/ReactionMechanismGenerator/RMG-Py
+  license: MIT
+  summary: "The ReactionMechanismGenerator Molecule Subpackage"

.rmgmolecule_conda/meta.yaml

@@ -0,0 +1,176 @@
+import sys
+import os
+from collections import OrderedDict
+
+try:
+    from distutils.core import setup
+    from distutils.extension import Extension
+except ImportError:
+    print("The distutils package is required to build or install RMG Py.")
+    raise
+
+try:
+    from Cython.Build import cythonize
+    from Cython.Compiler import Options
+except ImportError:
+    print("Cython (http://www.cython.org/) is required to build or install RMG Py.")
+    raise
+
+try:
+    import numpy
+except ImportError:
+    print("NumPy (http://numpy.scipy.org/) is required to build or install RMG Py.")
+    raise
+
+# Create annotated HTML files for each of the Cython modules
+Options.annotate = True
+
+directives = {
+    # Set input language version to python 3
+    "language_level": 3,
+    # Turn on profiling capacity for all Cython modules
+    # 'profile': True,
+    # Embed call signatures in cythonized files - enable when building documentation
+    # 'embedsignature': True,
+}
+
+
+main_ext_modules = [
+    # Molecules and molecular representations
+    Extension(
+        "rmgpy.molecule.atomtype",
+        ["rmgpy/molecule/atomtype.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.element",
+        ["rmgpy/molecule/element.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.graph",
+        ["rmgpy/molecule/graph.pyx"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.group",
+        ["rmgpy/molecule/group.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.molecule",
+        ["rmgpy/molecule/molecule.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.symmetry",
+        ["rmgpy/molecule/symmetry.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.vf2",
+        ["rmgpy/molecule/vf2.pyx"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.converter",
+        ["rmgpy/molecule/converter.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.translator",
+        ["rmgpy/molecule/translator.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.util",
+        ["rmgpy/molecule/util.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.inchi",
+        ["rmgpy/molecule/inchi.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.resonance",
+        ["rmgpy/molecule/resonance.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.pathfinder",
+        ["rmgpy/molecule/pathfinder.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.molecule.kekulize",
+        ["rmgpy/molecule/kekulize.pyx"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.constants",
+        ["rmgpy/constants.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.quantity",
+        ["rmgpy/quantity.py"],
+        include_dirs=["."],
+    ),
+    Extension(
+        "rmgpy.rmgobject",
+        ["rmgpy/rmgobject.pyx"],
+    ),
+]
+
+ext_modules = []
+if "install" in sys.argv:
+    # This is so users can still do simply `python setup.py install`
+    ext_modules.extend(main_ext_modules)
+if "main" in sys.argv:
+    # This is for `python setup.py build_ext main`
+    sys.argv.remove("main")
+    ext_modules.extend(main_ext_modules)
+if "minimal" in sys.argv:
+    # This starts with the full install list, but removes anything that has a pure python mode
+    # i.e. in only includes things whose source is .pyx
+    sys.argv.remove("minimal")
+    temporary_list = []
+    temporary_list.extend(main_ext_modules)
+    for module in temporary_list:
+        for source in module.sources:
+            if os.path.splitext(source)[1] == ".pyx":
+                ext_modules.append(module)
+
+# Remove duplicates while preserving order:
+ext_modules = list(OrderedDict.fromkeys(ext_modules))
+
+scripts = []
+
+modules = ["rmgpy.exceptions", "rmgpy.version"]
+
+__version__ = "1.0.0"
+
+import logging
+
+logging.error(ext_modules)
+# Initiate the build and/or installation
+setup(
+    name="RMG-Py",
+    version=__version__,
+    description="Reaction Mechanism Generator",
+    author="William H. Green and the RMG Team",
+    author_email="[email protected]",
+    url="http://reactionmechanismgenerator.github.io",
+    packages=[
+        "rmgpy.molecule",
+    ],
+    py_modules=modules,
+    scripts=scripts,
+    ext_modules=cythonize(
+        ext_modules,
+        build_dir="build",
+        compiler_directives=directives,
+    ),
+    include_dirs=[".", numpy.get_include()],
+)

rmgmolecule_setup.py

@@ -61,7 +61,12 @@
 from rdkit.Chem import AllChem
 
 from rmgpy.molecule.molecule import Atom, Molecule
-from rmgpy.qm.molecule import Geometry
+
+Geometry = None
+try:
+    from rmgpy.qm.molecule import Geometry
+except ImportError:
+    logging.info("Unable to import Geometry rmgpy.qm.molecule - feature disabled.")
 
 
 ################################################################################
@@ -437,6 +442,11 @@ def _generate_coordinates(self):
             # Generate the RDkit molecule from the RDkit molecule, use geometry
             # in order to match the atoms in the rdmol with the atoms in the
             # RMG molecule (which is required to extract coordinates).
+            if Geometry is None:
+                raise RuntimeError("""
+Missing rmgpy.qm.molecule.Geometry required for 2D coordinate generation.
+Please install the full version of RMG to use this function.
+                    """)
             self.geometry = Geometry(None, None, self.molecule, None)
 
             rdmol, rd_atom_idx = self.geometry.rd_build()

rmgpy/molecule/draw.py

@@ -1020,7 +1020,13 @@ def assign_representative_molecule(self):
 
     def assign_representative_species(self):
 
-        from rmgpy.species import Species
+        try:
+            from rmgpy.species import Species
+        except ImportError as ie:
+            raise RuntimeError(
+                "Cannot call Fragment.assign_representative_species() in rmgmolecule installation."
+                " Please install the full version of RMG."
+                ) from ie
         self.assign_representative_molecule()
         self.species_repr = Species(molecule=[self.mol_repr])
         self.symmetry_number = self.get_symmetry_number()

rmgpy/molecule/fragment.py

@@ -702,7 +702,13 @@ def _convert_3_atom_2_bond_path(start, mol):
     with a number of actions that reflect the changes in bond orders and unpaired
     electrons that the molecule should undergo.
     """
-    from rmgpy.data.kinetics.family import ReactionRecipe
+    try:
+        from rmgpy.data.kinetics.family import ReactionRecipe
+    except ImportError as ie:
+        raise RuntimeError(
+            "Cannot call inchi._convert_3_atom_2_bond_path() in rmgmolecule installation."
+            " Please install the full version of RMG."
+            ) from ie 
 
     def is_valid(mol):
         """Check if total bond order of oxygen atoms is smaller than 4."""