Merge pull request #379 from Electrostatics/nathan/378

Version 3.6.2 release candidate

.readthedocs.yaml

@@ -1,12 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: "3.8"
   install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - test
-        - dev
-    - method: setuptools
-      path: .
+    - requirements: docs/requirements.txt

docs/requirements.txt

@@ -0,0 +1,8 @@
+sphinx==5.3.0
+sphinx_rtd_theme==1.1.1
+sphinx_sitemap==2.5.1
+readthedocs-sphinx-search==0.1.1
+propka >= 3.5
+numpy
+pdbx
+mmcif_pdbx>=1.1.2

docs/source/releases.rst

@@ -2,9 +2,9 @@
 Release history
 ###############
 
-***************
-Current version
-***************
+******************
+3.6.2 (2023-12-31)
+******************
 
 Changes
 =======
@@ -14,7 +14,14 @@ Changes
 Fixes
 =====
 
-* Fixed broken link in documentation (`#363 <https://github.com/Electrostatics/pdb2pqr/issues/363>`_)
+* Fixed problem locating files with editable installations (`#6 <https://github.com/Electrostatics/pdb2pqr/issues/6>`_)
+* Fixed broken links in documentation (`#363 <https://github.com/Electrostatics/pdb2pqr/issues/363>`_)
+
+Known issues
+============
+
+* There is a confirmed issue with naming using the CHARMM force field for uncommon protonation states (`#358 <https://github.com/Electrostatics/pdb2pqr/issues/358>`_)
+* There is a potential problem adding hydrogens to non-experimental computer-generated structures (`#365 <https://github.com/Electrostatics/pdb2pqr/issues/375>`_)
 
 ******************
 3.6.1 (2023-03-12)

pdb2pqr/_version.py

@@ -5,4 +5,4 @@
 * we can import it in setup.py for the same reason
 * we can import it into your module
 """
-__version__ = "3.6.1"
+__version__ = "3.6.2"