From 31c286dc625b858b73e617d91430701a18563285 Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sun, 31 Dec 2023 17:30:06 -0800 Subject: [PATCH 1/6] Update requirements for readthedocs. --- .readthedocs.yaml | 39 +++++++++++++++++++++++++++++++-------- docs/requirements.txt | 4 ++++ 2 files changed, 35 insertions(+), 8 deletions(-) create mode 100644 docs/requirements.txt diff --git a/.readthedocs.yaml b/.readthedocs.yaml index b1897da..e952a46 100644 --- a/.readthedocs.yaml +++ b/.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 diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..7a9eb61 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,4 @@ +sphinx==5.3.0 +sphinx_rtd_theme==1.1.1 +sphinx_sitemap==2.5.1 +readthedocs-sphinx-search==0.1.1 \ No newline at end of file From a9eafea0127811eb15df259347b6cfaaf416a28a Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sun, 31 Dec 2023 17:30:19 -0800 Subject: [PATCH 2/6] Update release documentation. --- docs/source/releases.rst | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/docs/source/releases.rst b/docs/source/releases.rst index d9d00a0..961b2e3 100644 --- a/docs/source/releases.rst +++ b/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 `_) +* Fixed problem locating files with editable installations (`#6 `_) +* Fixed broken links in documentation (`#363 `_) + +Known issues +============ + +* There is a confirmed issue with naming using the CHARMM force field for uncommon protonation states (`#358 `_) +* There is a potential problem adding hydrogens to non-experimental computer-generated structures (`#365 `_) ****************** 3.6.1 (2023-03-12) From 697acbcbfc209f1be9b19c3d3fe7ff2cf59d9df0 Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sun, 31 Dec 2023 17:30:32 -0800 Subject: [PATCH 3/6] Update version number. --- pdb2pqr/_version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pdb2pqr/_version.py b/pdb2pqr/_version.py index 6b5aaf9..4622fbf 100644 --- a/pdb2pqr/_version.py +++ b/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" From 79ef8db98c6cb60a256fc1ff330519ca2a411764 Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sun, 31 Dec 2023 17:37:11 -0800 Subject: [PATCH 4/6] Update Sphinx requirements. --- docs/requirements.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 7a9eb61..628cc11 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,4 +1,5 @@ sphinx==5.3.0 sphinx_rtd_theme==1.1.1 sphinx_sitemap==2.5.1 -readthedocs-sphinx-search==0.1.1 \ No newline at end of file +readthedocs-sphinx-search==0.1.1 +propka \ No newline at end of file From 74974fa403f5db670ed26f4467c1fb1ac9aa2641 Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sun, 31 Dec 2023 17:49:05 -0800 Subject: [PATCH 5/6] Fix missing Sphinx dependency. --- docs/requirements.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 628cc11..efaa52e 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -2,4 +2,5 @@ sphinx==5.3.0 sphinx_rtd_theme==1.1.1 sphinx_sitemap==2.5.1 readthedocs-sphinx-search==0.1.1 -propka \ No newline at end of file +propka +numpy \ No newline at end of file From 251981acaba55093591752ce9c5e3e2180d64158 Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sun, 31 Dec 2023 18:07:30 -0800 Subject: [PATCH 6/6] Add more requirements/dependencies. --- docs/requirements.txt | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index efaa52e..a9f09eb 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -2,5 +2,7 @@ sphinx==5.3.0 sphinx_rtd_theme==1.1.1 sphinx_sitemap==2.5.1 readthedocs-sphinx-search==0.1.1 -propka -numpy \ No newline at end of file +propka >= 3.5 +numpy +pdbx +mmcif_pdbx>=1.1.2