work on fixing RTD error by exporting conda env file

ekwan · Mar 29, 2021 · 0b31171 · 0b31171
1 parent b50f1f0
commit 0b31171
Show file tree

Hide file tree

Showing 5 changed files with 27 additions and 5 deletions.
diff --git a/cctk/orca_file.py b/cctk/orca_file.py
@@ -262,11 +262,11 @@ def write_file(self, filename, molecule=None, header=None, variables=None, block
     @classmethod
     def write_molecule_to_file(cls, filename, molecule, header, variables=None, blocks=None, print_symbol=False):
         """
-        Write a ``.inp``file using the given molecule.
+        Write an ``.inp`` file using the given molecule.
 
         Args:
             filename (str): path to the new file
-            molecule (Molecule): which molecule to use -- a``Molecule`` object.
+            molecule (Molecule): which molecule to use -- a ``Molecule`` object.
             header (str): header for new file
             print_symbol (Bool): if atomic symbols should be printed instead of atomic numbers
         """

diff --git a/docs/cctk.rst b/docs/cctk.rst
@@ -36,10 +36,12 @@ Files
     :toctree: _autosummary 
 
     File <file.File>
-    GaussianJobType <gaussian_file.GaussianJobType>
     GaussianFile <gaussian_file.GaussianFile>
     MAEFile <mae_file.MAEFile>
     MOL2File <mol2_file.MOL2File>
+    OrcaFile <orca_file.OrcaFile>
+    PDBFile <pdb_file.PDBFile>
+    SIFile <si_file.SIFile>
     XYZFile <xyz_file.XYZFile>
 
 """""""""""""
@@ -49,9 +51,12 @@ Miscellaneous
 .. autosummary::
     :nosignatures:
     :toctree: _autosummary
-
+    
     Group <group.Group>
+    VibrationalMode <vibrational_mode.VibrationalMode>
     helper_functions
+    OneIndexedArray <array.OneIndexedArray>
+    LazyLineObject <lines.LazyLineObject>
 
 |br|
 
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -0,0 +1,15 @@
+name: chem
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3
+  - tabulate
+  - tqdm
+  - pandas
+  - matplotlib
+  - numpy
+  - xtb
+  - rdkit
+  - pytraj
+prefix: /opt/miniconda3/envs/chem
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -6,3 +6,4 @@ sphinx==3.5
 sphinx_bootstrap_theme
 pyahocorasick
 basis_set_exchange
+pyyaml
diff --git a/readthedocs.yml b/readthedocs.yml
@@ -16,7 +16,8 @@ formats: all
 python:
   version: 3.7
   install:
-    - requirements: docs/requirements.txt
+#    - requirements: docs/requirements.txt
+    - requirements: docs/environment.yml
 
 submodules:
   include: all