Merged
Conversation
lawrenceabird
force-pushed
the
lb/050126_docs
branch
from
b400c3d to
2522484
Compare
Leave tutorials in docs/source/tutorials/ so they are rendered by Sphinx. Copy them to docs/source/_static/tutorials to be downloaded
lawrenceabird
force-pushed
the
lb/050126_docs
branch
from
ba30dc0 to
2b4da40
Compare
justinh2002
pushed a commit
that referenced
this pull request
Feb 11, 2026
Add initial documentation infrastructure for pyISSM. `model.py` provides an example of correctly formatted docstrings. Summary of squashed commits: * Initial sphinx-quickstart * Initial workflow * Add PR trigger for testing * Remove shinx-apidoc dependency * Update permissions and add package dependencies * Redeploy pages * Redeploy docs * move docs/conf.py to docs/source/conf.py * Test removing files * Relax errors * Add index.rst to docs/source * Add sections * Specify package modules * Add placeholder top-level documentation * Update docs * Add doc link to README * Add comment for temporary fix in conf.py * Disable ISSM tests for testing * Update sidebar:Point to pyissm.rst not modules.rst * Attempt to modify structure * Add autodoc_default_options * Add docs link in README * Customise api structure * Update API page * Add top-level docstrings * Update Model.py docstrings * Update url/directory to be api, not generated * Update Model.py * Add tutorials & example notebook * Update tutorials paths * Move tutorials/ to source/tutorials * Try myst-nb rather than npsphinx * Add other pyissm.model classes * Update notebook warning block * Correct typo * Update myst options * Update warning syntax * Add download notebook button * Update html prior to move * Move tutorials/ to _static/tutorials * Move tutorials back from _static * Add CI to cp tutorials to _static for downloading Leave tutorials in docs/source/tutorials/ so they are rendered by Sphinx. Copy them to docs/source/_static/tutorials to be downloaded * Add helper for correct notebook path * Adjust path * Move download button to bottom * Update tutorials structure/location & rendering * mkdir before copying * Debug tutorials copy * Minor updates * Update README.md * Minor updates * Remove unneeded __all__ definition * Update link * Update pyissm.rst * Add __version__ for install confirmation * Update conf.py and docs.yml
justinh2002
pushed a commit
that referenced
this pull request
Feb 18, 2026
Add initial documentation infrastructure for pyISSM. `model.py` provides an example of correctly formatted docstrings. Summary of squashed commits: * Initial sphinx-quickstart * Initial workflow * Add PR trigger for testing * Remove shinx-apidoc dependency * Update permissions and add package dependencies * Redeploy pages * Redeploy docs * move docs/conf.py to docs/source/conf.py * Test removing files * Relax errors * Add index.rst to docs/source * Add sections * Specify package modules * Add placeholder top-level documentation * Update docs * Add doc link to README * Add comment for temporary fix in conf.py * Disable ISSM tests for testing * Update sidebar:Point to pyissm.rst not modules.rst * Attempt to modify structure * Add autodoc_default_options * Add docs link in README * Customise api structure * Update API page * Add top-level docstrings * Update Model.py docstrings * Update url/directory to be api, not generated * Update Model.py * Add tutorials & example notebook * Update tutorials paths * Move tutorials/ to source/tutorials * Try myst-nb rather than npsphinx * Add other pyissm.model classes * Update notebook warning block * Correct typo * Update myst options * Update warning syntax * Add download notebook button * Update html prior to move * Move tutorials/ to _static/tutorials * Move tutorials back from _static * Add CI to cp tutorials to _static for downloading Leave tutorials in docs/source/tutorials/ so they are rendered by Sphinx. Copy them to docs/source/_static/tutorials to be downloaded * Add helper for correct notebook path * Adjust path * Move download button to bottom * Update tutorials structure/location & rendering * mkdir before copying * Debug tutorials copy * Minor updates * Update README.md * Minor updates * Remove unneeded __all__ definition * Update link * Update pyissm.rst * Add __version__ for install confirmation * Update conf.py and docs.yml
justinh2002
added a commit
that referenced
this pull request
Feb 25, 2026
…9, 3201–3206, 3480) (#114) * Update Tests (#113) Update previously failing CI tests Summary of squashed commits: * Update previously failing tests & remove exclude Update tests that were previously failing and remove them from the exclude list. * test443 - Update regionalmask * Update regionaloutput -- prevent mask overwrite When marshalling the file, self.mask was always being written using self.maskexpstring, so it was over-writing any existing self.mask definition. If the string was empty, the returned mask would be empty. Use None rather than empty string for the mask definition and add additional condition to only update self.mask if self.maskexpstring is provided. * Update test443 - Assign collapsed model to md2 md2.collapse() returns a collapsed model. It must be re-assigned to md2 * Initial documentation Infrastructure (#88) Add initial documentation infrastructure for pyISSM. `model.py` provides an example of correctly formatted docstrings. Summary of squashed commits: * Initial sphinx-quickstart * Initial workflow * Add PR trigger for testing * Remove shinx-apidoc dependency * Update permissions and add package dependencies * Redeploy pages * Redeploy docs * move docs/conf.py to docs/source/conf.py * Test removing files * Relax errors * Add index.rst to docs/source * Add sections * Specify package modules * Add placeholder top-level documentation * Update docs * Add doc link to README * Add comment for temporary fix in conf.py * Disable ISSM tests for testing * Update sidebar:Point to pyissm.rst not modules.rst * Attempt to modify structure * Add autodoc_default_options * Add docs link in README * Customise api structure * Update API page * Add top-level docstrings * Update Model.py docstrings * Update url/directory to be api, not generated * Update Model.py * Add tutorials & example notebook * Update tutorials paths * Move tutorials/ to source/tutorials * Try myst-nb rather than npsphinx * Add other pyissm.model classes * Update notebook warning block * Correct typo * Update myst options * Update warning syntax * Add download notebook button * Update html prior to move * Move tutorials/ to _static/tutorials * Move tutorials back from _static * Add CI to cp tutorials to _static for downloading Leave tutorials in docs/source/tutorials/ so they are rendered by Sphinx. Copy them to docs/source/_static/tutorials to be downloaded * Add helper for correct notebook path * Adjust path * Move download button to bottom * Update tutorials structure/location & rendering * mkdir before copying * Debug tutorials copy * Minor updates * Update README.md * Minor updates * Remove unneeded __all__ definition * Update link * Update pyissm.rst * Add __version__ for install confirmation * Update conf.py and docs.yml * Clean unused directories; move files/ to assets/ * only run ad 3015:3019 * test run 3015 * add test3019.py * nan debugger * testing * amend autodiff isnan handling for fo forward * i gotta test * test * amend to get ~isempty * make debugger not break on lists * Fix autodiff consistency failure caused by isnan on non-numeric fields * i delete you * i delete you * am trying to fix this issue * comment debugger out * fixing this or else * fix how indices are stored * revert autodiff class handling of index builder * revert check_field * revert check_field * revert * test setting fov_forward_indices as scalar * test * dont need to set fov_reverse index * allow vector indices? * test * amend to like matlab * amend to like matlab * amend to like matlab * if codipack flag add * test * revert and fix * test * conversion * add nods * 3480 * 4380 * amend * fix * a fair few exclusions * add 3201 * fix * add cfsurfacelogvel.py * modify test3201.py * modify test3201.py * added adm1qn3inversion * amend * done * done * build statement * build statement * add all my tests * adm1qn3 added and refined to match the other classes * add cfsurfacesquare.py * add cfsurfacesquare and cfsurfacesquare transient in one class * add all AD runs * amend package imports * add cfsurfacelogvel * remove duplicate classes * ammend toolkits * False flag * update toolkits * make changes * change mattype to mpisparse * fix 3201 * fix * test3201.py * add stuff * did it fail really now? * should be mpisparse * add nods * test * start at 0 * change counter * check * change * add test * change indep.type to element * element based * element based * chagne abck to vertex * chagne abck to vertex * change ts1 * change ts1 * fix tests * fix rheology marshalling when we have dimension 2 * fix to .steps * the conditional check for self.rheology_B is fixed, ref matice.py * fix loop * undo comment out * rip syntax * start rheology with 2D array * add cflevelsetmisfit * ammend innit * amend cflevelsetmisfit class * removed repr * fix cflevelmisfit usage * amend depdent * update * maybe missed a counter? * amend 3203 and 3204 * fix change * make changes to 3204 and 3480 * make changes to 3204 and 3480 * amend how rheology is initialized * test now * add * add dep.nods * noway? * check to see if right * test * test * fix control size * fix control size * rewrite how fields are stacked and division by yts * add reinitializelevelset * add reinitializelevelset * dont index 2 rows of the array * dont index 2 rows of the array * push * push * proper class usage * fix * remove reinitialization * amend imports * add test3607 * wrong import * isoline passes a couple args * whoops * fix * fix weight initi * add 3206 * exclude 3203 * cherry-pick commit that fixes test2303.py * include 3203 back again * change cf* class to cf * update import * change where isoline() sits * fix * amend where reinitializelevelset lives * add staging dir * remove self * remove imports * remove staging dir files from parent dir * amend pos * change * update CI.yml * classrename * amend writedata call * this should work now? * rev and fix * legacy fallback * change * renamed dirs * move staging files to general tests * address comments * change the imports --------- Co-authored-by: Lawrence Bird <lawrence.bird@anu.edu.au>
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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.
PR for testing documentation deployment
Documentation is generated here: https://access-nri.github.io/pyISSM/