Update dependencies, available readers, wildcard selections

.gitignore

@@ -22,7 +22,8 @@ doc/build
 *.so
 
 # Ignore generated docs
-# *.txt
+# */**/*.txt
+# !requirements.txt
 
 # ignore generated files
 *.vmd

.readthedocs.yml

@@ -0,0 +1,22 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: doc/source/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+
+conda:
+  environment: environment.yml

doc/source/conf.py

@@ -54,11 +54,12 @@ def sort_authors(filename):
 # -- Scripts -----------------------------------------------
 # Get Travis to regenerate txt tables by re-running scripts
 # before deploying docs.
-# Turned off for now as 0.21.0 not released yet.
 # This allows us to gitignore .txt files as well as
 # auto-recreate tables for each deployment.
 # Turn off if using sphinx_autobuild as this will autobuild
 # to infinity.
+# TURNED OFF FOR NOW until we sort out how versioned docs
+# work and how we will install MDAnalysis + dependencies
 #
 # subprocess.call('./scripts/generate_all.sh')
 
@@ -174,6 +175,8 @@ def sort_authors(filename):
                        'https://docs.scipy.org/doc/numpy/': None,
                        'https://www.mdanalysis.org/docs/': None,
                        'https://docs.pytest.org/en/latest/': None,
+                       'https://chemfiles.org/chemfiles.py/latest/': None,
+                       'http://parmed.github.io/ParmEd/html/': None,
                        }
 
 # nbsphinx

doc/source/contributing_code.rst

@@ -203,31 +203,37 @@ Building MDAnalysis
 -------------------
 
 Make sure that you have :ref:`cloned the repository <forking-code-repo>`  
-and activated your virtual environment. First we need to install dependencies:
+and activated your virtual environment. First we need to install dependencies. If you're using conda, you'll need a mix of conda and pip installations:
 
     .. code-block:: bash
 
-        # if using conda
         conda install -c biobuilds -c conda-forge \
-            pip cython numpy mmtf-python mock six biopython \
-            networkx cython matplotlib scipy griddataformats \
-            hypothesis gsd codecov "seaborn>=0.7.0,<=0.9" \
-            clustalw=2.1 netcdf4 scikit-learn "joblib>=0.12"\
-            psutil pytest
+            biopython chemfiles clustalw==2.1 codecov cython \
+            griddataformats gsd hypothesis "joblib>=0.12" \
+            matplotlib mmtf-python mock netcdf4 networkx \
+            "numpy>=1.17.3" psutil pytest scikit-learn scipy \
+            "seaborn>=0.7.0,<0.9" sphinx==1.8.5 "tidynamics>=1.0.0" \
+            "tqdm>=4.43.0"
 
         # if using conda with python 3.7 or 3.8, also run
         conda install -c conda-forge parmed
 
         # if using conda with other versions of python, also run
         pip install parmed
 
+        # documentation dependencies
+        pip install sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0
+
+If you're using pip, it is a little simpler. However, some packages such as ``clustalw`` are not available via pip.
+
     .. code-block:: bash
 
-        # if using pip and virtualenv
-        pip install cython numpy mmtf-python mock six biopython \
-            networkx cython matplotlib scipy griddataformats \
-            hypothesis gsd codecov "seaborn>=0.7.0,<=0.9" \
-            netcdf4 scikit-learn "joblib>=0.12" parmed psutil pytest
+        pip install biopython chemfiles codecov cython \
+          griddataformats gsd hypothesis "joblib>=0.12" matplotlib \
+          msmb_theme==1.2.0 netcdf4 networkx "numpy>=1.17.3" \
+          parmed psutil pytest scikit-learn scipy "seaborn>=0.7.0,<0.9" \
+          sphinx==1.8.5 sphinx_rtd_theme "tidynamics>=1.0.0" \
+          "tqdm>=4.43.0"
 
 Ensure that you have a working C/C++ compiler (e.g. gcc or clang). You will also need Python ≥ 3.4. We will now install MDAnalysis. 
 
@@ -555,17 +561,7 @@ Building the documentation
 
 The online documentation is generated from the pages in ``mdanalysis/package/doc/sphinx/source/documentation_pages``. The documentation for the current release are hosted at www.mdanalysis.org/docs, while the development version is at www.mdanalysis.org/mdanalysis/. 
 
-In order to build the documentation, you must first :ref:`clone the main MDAnalysis repo <forking-code-repo>`. :ref:`Set up a virtual environment <create-virtual-environment>` in the same way as you would for the code (you can use the same environment as you do for the code). You will need to install several packages for the docs.
-
-    .. code-block:: bash
-
-        pip install sphinx sphinx-sitemap sphinx_rtd_theme
-
-In addition, build the development version of MDAnalysis (if you haven't done this already):
-
-    .. code-block:: bash
-
-        pip install -e .
+In order to build the documentation, you must first :ref:`clone the main MDAnalysis repo <forking-code-repo>`. :ref:`Set up a virtual environment <create-virtual-environment>` in the same way as you would for the code (you should typically use the same environment as you do for the code). Build the development version of MDAnalysis. 
 
 Then, generate the docs with:
 

doc/source/formats/coordinate_readers.txt

@@ -1,35 +1,46 @@
-=====================================  =========================================  ============  ========
-File type                              Description                                Velocities    Forces
-=====================================  =========================================  ============  ========
-:ref:`ARC <TXYZ-format>`               Tinker file
-:ref:`CONFIG <CONFIG-format>`          DL_Poly CONFIG file                        ✓
-:ref:`CRD <CRD-format>`                CHARMM CARD file
-:ref:`CRDBOX <TRJ-format>`             AMBER ASCII trajectories
-:ref:`DATA <DATA-format>`              LAMMPS data file                           ✓
-:ref:`DCD <DCD-format>`                CHARMM, NAMD, or LAMMPS binary trajectory
-:ref:`DMS <DMS-format>`                DESRES Molecular Structure file            ✓
-:ref:`ENT <PDB-format>`                Standard PDB file
-:ref:`GMS <GMS-format>`                GAMESS file
-:ref:`GRO <GRO-format>`                GROMACS structure file                     ✓
-:ref:`GSD <GSD-format>`                HOOMD GSD file
-:ref:`HISTORY <HISTORY-format>`        DL_Poly HISTORY file                       ✓
-:ref:`INPCRD <INPCRD-format>`          AMBER restart file
-:ref:`LAMMPS <LAMMPS-format>`          a LAMMPS DCD trajectory
-:ref:`LAMMPSDUMP <LAMMPSDUMP-format>`  LAMMPS ascii dump file
-:ref:`MDCRD <TRJ-format>`              AMBER ASCII trajectories
-:ref:`MMTF <MMTF-format>`              MMTF file
-:ref:`MOL2 <MOL2-format>`              Tripos MOL2 file
-:ref:`NC <NCDF-format>`                AMBER NETCDF format                        ✓             ✓
-:ref:`NCDF <NCDF-format>`              AMBER NETCDF format                        ✓             ✓
-:ref:`PDB <PDB-format>`                Standard PDB file
-:ref:`PDBQT <PDBQT-format>`            PDBQT file
-:ref:`PQR <PQR-format>`                PQR file
-:ref:`RESTRT <INPCRD-format>`          AMBER restart file
-:ref:`TRJ <TRJ-format>`                AMBER ASCII trajectories
-:ref:`TRR <TRR-format>`                GROMACS TRR trajectory                     ✓             ✓
-:ref:`TRZ <TRZ-format>`                IBIsCO or YASP binary trajectory           ✓
-:ref:`TXYZ <TXYZ-format>`              Tinker file
-:ref:`XPDB <XPDB-format>`              Extended PDB file
-:ref:`XTC <XTC-format>`                GROMACS compressed trajectory
-:ref:`XYZ <XYZ-format>`                XYZ file
-=====================================  =========================================  ============  ========
+..
+    Generated by gen_format_overview_classes.py
+
+.. table:: Table of supported coordinate readers and the information read
+
+    =====================================  ====================================================================  ============  ========
+    File type                              Description                                                           Velocities    Forces
+    =====================================  ====================================================================  ============  ========
+    :ref:`ARC <TXYZ-format>`               Tinker file
+    :ref:`CHEMFILES <CHEMFILES-format>`    use readers from `chemfiles <https://chemfiles.org/>`_ library
+    :ref:`CONFIG <CONFIG-format>`          DL_Poly CONFIG file                                                   ✓
+    :ref:`COOR <COOR-format>`              NAMD binary restart file
+    :ref:`CRD <CRD-format>`                CHARMM CARD file
+    :ref:`CRDBOX <TRJ-format>`             AMBER ASCII trajectories
+    :ref:`DATA <DATA-format>`              LAMMPS data file                                                      ✓
+    :ref:`DCD <DCD-format>`                CHARMM, NAMD, or LAMMPS binary trajectory
+    :ref:`DMS <DMS-format>`                DESRES Molecular Structure file                                       ✓
+    :ref:`ENT <PDB-format>`                Standard PDB file
+    :ref:`FHIAIMS <IN-format>`             FHI-aims input file                                                   ✓
+    :ref:`GMS <GMS-format>`                GAMESS file
+    :ref:`GRO <GRO-format>`                GROMACS structure file                                                ✓
+    :ref:`GSD <GSD-format>`                HOOMD GSD file
+    :ref:`HISTORY <HISTORY-format>`        DL_Poly HISTORY file                                                  ✓
+    :ref:`IN <IN-format>`                  FHI-aims input file                                                   ✓
+    :ref:`INPCRD <INPCRD-format>`          AMBER restart file
+    :ref:`LAMMPS <LAMMPS-format>`          a LAMMPS DCD trajectory
+    :ref:`LAMMPSDUMP <LAMMPSDUMP-format>`  LAMMPS ascii dump file
+    :ref:`MDCRD <TRJ-format>`              AMBER ASCII trajectories
+    :ref:`MMTF <MMTF-format>`              MMTF file
+    :ref:`MOL2 <MOL2-format>`              Tripos MOL2 file
+    :ref:`NAMDBIN <COOR-format>`           NAMD binary restart file
+    :ref:`NC <NCDF-format>`                AMBER NETCDF format                                                   ✓             ✓
+    :ref:`NCDF <NCDF-format>`              AMBER NETCDF format                                                   ✓             ✓
+    :ref:`PARMED <PARMED-format>`          `ParmEd <http://parmed.github.io/ParmEd/html/index.html>`_ Structure
+    :ref:`PDB <PDB-format>`                Standard PDB file
+    :ref:`PDBQT <PDBQT-format>`            PDBQT file
+    :ref:`PQR <PQR-format>`                PQR file
+    :ref:`RESTRT <INPCRD-format>`          AMBER restart file
+    :ref:`TRJ <TRJ-format>`                AMBER ASCII trajectories
+    :ref:`TRR <TRR-format>`                GROMACS TRR trajectory                                                ✓             ✓
+    :ref:`TRZ <TRZ-format>`                IBIsCO or YASP binary trajectory                                      ✓
+    :ref:`TXYZ <TXYZ-format>`              Tinker file
+    :ref:`XPDB <XPDB-format>`              Extended PDB file
+    :ref:`XTC <XTC-format>`                GROMACS compressed trajectory
+    :ref:`XYZ <XYZ-format>`                XYZ file
+    =====================================  ====================================================================  ============  ========

doc/source/formats/coordinates.rst

@@ -3,6 +3,4 @@
 Coordinates
 ===========
 
-.. table:: Table of supported coordinate readers and the information read
-
-    .. include:: coordinate_readers.txt
+.. include:: coordinate_readers.txt