Improve docs #803
Merged
Improve docs #803
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
mgiulini
added
enhancement
rvhonorato
requested changes
Feb 20, 2024
There was a problem hiding this comment.
Nice!
When you run the sphinx commands it generates a lot of these .rst files that are not in the .gitignore, so I'm guessing you edit it or should they be in the repository?
On branch improve_docs
Your branch is up to date with 'origin/improve_docs'.
Untracked files:
(use "git add <file>..." to include in what will be committed)
docs/haddock.clis.cli.rst
docs/haddock.clis.cli_analyse.rst
docs/haddock.clis.cli_bm.rst
docs/haddock.clis.cli_cfg.rst
docs/haddock.clis.cli_clean.rst
docs/haddock.clis.cli_cp.rst
docs/haddock.clis.cli_dmn.rst
docs/haddock.clis.cli_mpi.rst
docs/haddock.clis.cli_pp.rst
docs/haddock.clis.cli_re.rst
docs/haddock.clis.cli_restraints.rst
docs/haddock.clis.cli_score.rst
docs/haddock.clis.cli_traceback.rst
docs/haddock.clis.cli_unpack.rst
docs/haddock.clis.re.clustfcc.rst
docs/haddock.clis.re.clustrmsd.rst
docs/haddock.clis.re.rst
docs/haddock.clis.re.score.rst
docs/haddock.clis.restraints.active_passive_to_ambig.rst
docs/haddock.clis.restraints.passive_from_active.rst
docs/haddock.clis.restraints.restrain_bodies.rst
docs/haddock.clis.restraints.rst
docs/haddock.clis.restraints.validate_tbl.rst
docs/haddock.clis.rst
docs/haddock.core.cns_paths.rst
docs/haddock.core.defaults.rst
docs/haddock.core.exceptions.rst
docs/haddock.core.rst
docs/haddock.core.supported_molecules.rst
docs/haddock.core.typing.rst
docs/haddock.gear.clean_steps.rst
docs/haddock.gear.config.rst
docs/haddock.gear.expandable_parameters.rst
docs/haddock.gear.extend_run.rst
docs/haddock.gear.greetings.rst
docs/haddock.gear.haddockmodel.rst
docs/haddock.gear.parameters.rst
docs/haddock.gear.prepare_run.rst
docs/haddock.gear.preprocessing.rst
docs/haddock.gear.restart_run.rst
docs/haddock.gear.rst
docs/haddock.gear.validations.rst
docs/haddock.gear.yaml2cfg.rst
docs/haddock.gear.zerofill.rst
docs/haddock.libs.libalign.rst
docs/haddock.libs.libcli.rst
docs/haddock.libs.libclust.rst
docs/haddock.libs.libcns.rst
docs/haddock.libs.libfunc.rst
docs/haddock.libs.libhpc.rst
docs/haddock.libs.libinteractive.rst
docs/haddock.libs.libio.rst
docs/haddock.libs.liblog.rst
docs/haddock.libs.libmath.rst
docs/haddock.libs.libmpi.rst
docs/haddock.libs.libontology.rst
docs/haddock.libs.libparallel.rst
docs/haddock.libs.libpdb.rst
docs/haddock.libs.libplots.rst
docs/haddock.libs.librestraints.rst
docs/haddock.libs.libstructure.rst
docs/haddock.libs.libsubprocess.rst
docs/haddock.libs.libtimer.rst
docs/haddock.libs.libutil.rst
docs/haddock.libs.libworkflow.rst
docs/haddock.libs.rst
docs/haddock.modules.analysis.alascan.rst
docs/haddock.modules.analysis.alascan.scan.rst
docs/haddock.modules.analysis.caprieval.capri.rst
docs/haddock.modules.analysis.caprieval.rst
docs/haddock.modules.analysis.clustfcc.clustfcc.rst
docs/haddock.modules.analysis.clustfcc.rst
docs/haddock.modules.analysis.clustrmsd.clustrmsd.rst
docs/haddock.modules.analysis.clustrmsd.rst
docs/haddock.modules.analysis.contactmap.contmap.rst
docs/haddock.modules.analysis.contactmap.rst
docs/haddock.modules.analysis.ilrmsdmatrix.ilrmsd.rst
docs/haddock.modules.analysis.ilrmsdmatrix.rst
docs/haddock.modules.analysis.rmsdmatrix.rmsd.rst
docs/haddock.modules.analysis.rmsdmatrix.rst
docs/haddock.modules.analysis.rst
docs/haddock.modules.analysis.seletop.rst
docs/haddock.modules.analysis.seletopclusts.rst
docs/haddock.modules.extras.exit.rst
docs/haddock.modules.extras.rst
docs/haddock.modules.refinement.emref.rst
docs/haddock.modules.refinement.flexref.rst
docs/haddock.modules.refinement.mdref.rst
docs/haddock.modules.refinement.rst
docs/haddock.modules.sampling.gdock.rst
docs/haddock.modules.sampling.lightdock.rst
docs/haddock.modules.sampling.rigidbody.rst
docs/haddock.modules.sampling.rst
docs/haddock.modules.scoring.emscoring.rst
docs/haddock.modules.scoring.mdscoring.rst
docs/haddock.modules.scoring.rst
docs/haddock.modules.topology.rst
docs/haddock.modules.topology.topoaa.rst
docs/haddock.modules.topology.topocg.rst
nothing added to commit but untracked files present (use "git add" to track)
Other than that it looks functional to me.
rvhonorato
reviewed
Feb 20, 2024
basically the configuration file calls this |
|
those are generated after |
no, as they should not belong to the docs folder but rather moved to the subdirectories (which are gitignored). I added an mkdir statement for the case in which you do not have such subdirectories, can you remove the files and try again? |
rvhonorato
approved these changes
Feb 21, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
You are about to submit a new Pull Request. Before continuing make sure you read the contributing guidelines and that you comply with the following criteria:
toxtests pass. Runtoxcommand inside the repository folder-test.cfgexamples execute without errors. Insideexamples/runpython run_tests.py -bCloses #802 . This PR is supposed to substantially improve the autogenerated documentation created when running
tox -e docs. More specifically:buiild_defaults_rstsis adapted to move and prettify the rst files in thedocsfolder