From 10c7a15fa10aa6566a474fbdb0316bc7bcce3079 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Tue, 4 Feb 2025 10:25:12 -0600 Subject: [PATCH 1/3] Fix docs builds --- .readthedocs.yml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 6bfaa9bb..38251abf 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,14 +1,17 @@ -# .readthedocs.yml - version: 2 + build: os: ubuntu-20.04 tools: python: mambaforge-4.10 +sphinx: + configuration: docs/conf.py + fail_on_warning: true + # Build PDF in addition to default HTML and JSON formats: - pdf conda: - environment: devtools/conda-envs/docs.yaml \ No newline at end of file + environment: devtools/conda-envs/docs.yaml From 57baaf3476fcf536a5b02f463d91a4acfa3b9db9 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Tue, 11 Feb 2025 07:34:45 -0600 Subject: [PATCH 2/3] Update config --- .readthedocs.yml => .readthedocs.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) rename .readthedocs.yml => .readthedocs.yaml (66%) diff --git a/.readthedocs.yml b/.readthedocs.yaml similarity index 66% rename from .readthedocs.yml rename to .readthedocs.yaml index 38251abf..18e95236 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yaml @@ -3,15 +3,19 @@ version: 2 build: os: ubuntu-20.04 tools: - python: mambaforge-4.10 + python: "mambaforge-4.10" + +python: + install: + - method: pip + path: . + +conda: + environment: devtools/conda-envs/docs.yaml sphinx: configuration: docs/conf.py fail_on_warning: true -# Build PDF in addition to default HTML and JSON formats: - - pdf - -conda: - environment: devtools/conda-envs/docs.yaml +- pdf From ddad3aa0cabfc83c3b84b33d79a17e7b43508e99 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Tue, 11 Feb 2025 08:25:25 -0600 Subject: [PATCH 3/3] Update Sphinx config, broken links --- .readthedocs.yaml | 2 +- devtools/conda-envs/docs.yaml | 2 +- docs/api.rst | 39 ++++++++--------------------------- docs/conf.py | 17 ++++++++------- 4 files changed, 21 insertions(+), 39 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 18e95236..9d2b36cc 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -15,7 +15,7 @@ conda: sphinx: configuration: docs/conf.py - fail_on_warning: true + fail_on_warning: false formats: - pdf diff --git a/devtools/conda-envs/docs.yaml b/devtools/conda-envs/docs.yaml index cc98450b..253dbbb2 100644 --- a/devtools/conda-envs/docs.yaml +++ b/devtools/conda-envs/docs.yaml @@ -13,7 +13,7 @@ dependencies: - setuptools # Sphinx specific - - sphinx >=4.4,<5.0 + - sphinx =6 - nbsphinx - nbsphinx-link - sphinx_rtd_theme diff --git a/docs/api.rst b/docs/api.rst index c285a1c3..09027b9a 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -6,7 +6,7 @@ Below is an outline of the API for ``openff-qcsubmit``. See the examples for det .. warning:: The ``openff-qcsubmit`` package is still pre-alpha, so the API is still in flux. Datasets --------- +"""""""" .. currentmodule:: openff.qcsubmit.datasets .. autosummary:: @@ -21,8 +21,6 @@ Datasets TorsionDriveEntry FilterEntry -.. _factories: - Factories """"""""" @@ -65,7 +63,7 @@ Constraints PositionConstraintSet Results -------- +""""""" .. currentmodule:: openff.qcsubmit.results .. autosummary:: @@ -79,8 +77,8 @@ Results TorsionDriveResult TorsionDriveResultCollection -Filters -""""""" +Results Filters +""""""""""""""" .. currentmodule:: openff.qcsubmit.results.filters .. autosummary:: @@ -89,8 +87,6 @@ Filters ResultFilter CMILESResultFilter - ResultRecordFilter - ResultRecordGroupFilter SMILESFilter SMARTSFilter ChargeFilter @@ -103,25 +99,9 @@ Filters ConformerRMSDFilter MinimumConformersFilter -Caching -""""""" - -.. currentmodule:: openff.qcsubmit.results.caching -.. autosummary:: - :nosignatures: - :toctree: api/generated/ - - clear_results_caches - batched_indices - cached_fractal_client - cached_query_procedures - cached_query_molecules - cached_query_basic_results - cached_query_optimization_results - cached_query_torsion_drive_results Workflow Components -------------------- +""""""""""""""""""" .. currentmodule:: openff.qcsubmit.workflow_components .. autosummary:: @@ -183,7 +163,7 @@ State Enumeration ScanEnumerator Workflow Utilities -""""" +"""""""""""""""""" .. currentmodule:: openff.qcsubmit.workflow_components .. autosummary:: @@ -201,7 +181,7 @@ Workflow Utilities TorsionIndexer Common Structures ------------------ +""""""""""""""""" .. currentmodule:: openff.qcsubmit.common_structures .. autosummary:: @@ -216,14 +196,13 @@ Common Structures QCSpec QCSpecificationHandler IndexCleaner - ClientHandler Metadata MoleculeAttributes SCFProperties CommonBase Utilities ---------- +""""""""" .. currentmodule:: openff.qcsubmit.utils .. autosummary:: @@ -234,7 +213,7 @@ Utilities portal_client_manager Exceptions ----------- +"""""""""" .. currentmodule:: openff.qcsubmit.exceptions .. autosummary:: diff --git a/docs/conf.py b/docs/conf.py index 872e6c41..3abd7bf6 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -15,6 +15,8 @@ import os import sys +import openff.qcsubmit + sys.path.insert(0, os.path.abspath(os.pardir)) @@ -25,9 +27,9 @@ author = "Open Force Field Consortium" # The short X.Y version -version = "" +version = openff.qcsubmit.__version__ # The full version, including alpha/beta/rc tags -release = "" +release = openff.qcsubmit.__version__ # -- General configuration --------------------------------------------------- @@ -100,11 +102,12 @@ "https://open-forcefield-toolkit.readthedocs.io/en/latest/", None, ), - "qcportal": ("http://docs.qcarchive.molssi.org/projects/qcportal/en/latest/", None), - "qcelemental": ( - "http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/", - None, - ), + # Broken + # "qcportal": ("http://docs.qcarchive.molssi.org/projects/qcportal/en/latest/", None), + # "qcelemental": ( + # "http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/", + # None, + # ), "openff.docs": ( "https://docs.openforcefield.org/en/latest/", None,