make CLI starting guide easier to find from the landing page#1787
Merged
make CLI starting guide easier to find from the landing page#1787
Conversation
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1787 +/- ##
==========================================
- Coverage 95.27% 93.01% -2.26%
==========================================
Files 201 201
Lines 17589 17589
==========================================
- Hits 16758 16361 -397
- Misses 831 1228 +397
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
IAlibay
requested changes
Jan 12, 2026
IAlibay
approved these changes
Jan 13, 2026
Contributor
Author
|
blocked by #1792, I want to check that everything renders properly in the preview before merging. |
auto-merge was automatically disabled
January 15, 2026 20:39
Pull request was converted to draft
…e_quickstart_easier_to_find
|
🚨 API breaking changes detected! 🚨 |
7 tasks
atravitz
added a commit
that referenced
this pull request
Feb 5, 2026
* make CLI starting guide easier to find from the landing page * Python API -> API Docs * bump ci * bump example notebooks pin to 2026.01.26 * change a word * clarifying language
atravitz
added a commit
that referenced
this pull request
Feb 5, 2026
* update install instructions (#1744) * update manifest to include all .gz files (#1746) * update manifest to include all .gz files * add min openmmforcefields pin * bump cuda version to 11.8 (#1749) * fix deprecation warning on view_components_3d (#1750) * expose KartografAtomMapper alongside other AtomMappers (#1751) * fix psutils import (#1779) * fix psutils import * swap import order * [pre-commit.ci] pre-commit autoupdate (#1778) updates: - [github.com/tox-dev/pyproject-fmt: v2.8.0 → v2.11.1](tox-dev/pyproject-fmt@v2.8.0...v2.11.1) - [github.com/astral-sh/ruff-pre-commit: v0.13.3 → v0.14.10](astral-sh/ruff-pre-commit@v0.13.3...v0.14.10) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Disable NAGL as a partial charge backend when OEToolkit is installed but not chosen as the registry backend. (#1762) * NAGL can no longer be used with oechem installed if you are using the rdkit backend. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * rename openfecli fixture to avoid duplication with openfe fixture (#1755) Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * openfe gather: add progress bar for loading JSONs (#1786) * all the profiling * make progress bar pretty * revert typing thing * news * all the profiling * make progress bar pretty * revert typing thing * news * update expected outputs * update expected outputs * add dill mock to fix openfe docs build (#1792) * Fix issue 1795 (#1796) * Update method name in CLI YAML documentation * Fix command option case in CLI YAML guide * manually add absolute settings news item to changelog (#1821) * manually add absolute settings news item to changelog * add link * Fixes docstring to clarify argument does not have a default (#1819) * Fixes docstring to clarify argument does not have a default * Modernize typing * fix ligand network cropping bug (#1822) * fix ligand network cropping bug * move to upstream func * whitespace * fix pydantic deprecation of copy method * fix pydantic deprecation of dict method - septop (#1831) * Updated CHANGELOG for 1.8.1 * fix changelog links * add openeye w/ python 3.13 test to CI (#1745) * add openeye w/ python 3.13 test to CI * only run openeye on unbuntu w/ python 3.13 * add explicit openeye no * bump python version for conda cron (#1748) * remove mypy rdkit pin (#1753) * remove mypy rdkit pin * try more explicit import * Revert "try more explicit import" This reverts commit 00cc2a3. * disallow attr-defined error code * try globally disabling attr-defined * try specific override * per-line ignores * Make the multistate hybrid topology samplers not require the HybridTopologyFactory (#1768) * make hybrid samplers not rely on htf but instead on the system & positions. * Migrate validation to Protocol._validate in HybridTopologyProtocol (#1740) * Migrate & add validation to Protocol._validate for hybrid topology Protocol --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk> * Move rfe protocol (#1769) Move RFE protocol files around * HybridTop Unit methods (#1770) * Break down the Hybrid Top protocol unit into various methods. --------- Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> * Have two separate system generators for state A & B in hybrid protocol (#1772) Make it so that the states A and B are generated using two different SystemGenerator objects, allowing for partial charge transformations. * HybridTop structural analysis via API rather than CLI (#1771) * change structural analysis from using CLI to using API * making some language clearer on github-facing things (#1758) * making some language clearer on github-facing things * : * add pre-commit link * clean up * Moving AFE Protocols around a bit (#1775) * move the protocols results to a single file and deduplicate * rename base units file * move units out of method files * move a few things in init * Create setup, run, and analysis units for HybridTop Protocol (#1773) * Turn Hybrid Topology protocol into 3 units. --------- Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * update docs for multiple protocol units (#1793) * Update docstring for hybridtop classes (#1794) * Update docstring for classes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Small improvement in RelativeHybridTopologyProtocol docstring (#1797) Updated class docstring to clarify the use of Hybrid Topology scheme. * turn off zenodo retry (#1802) * turn off zenodo retry * remove retry_if_failed arg * only run CI on macos python 3.12 (#1803) * Turn AFE protocols into multiple units (#1776) * Split the AFE protocol units into setup, simulation, and analysis. * move to src layout (#1805) * Move openfe project layout to `src`. * Temporarily build pooch from main w/ hotfix (#1806) * build with pooch@main to see if hotfix works * add link * make CLI starting guide easier to find from the landing page (#1787) * make CLI starting guide easier to find from the landing page * Python API -> API Docs * bump ci * bump example notebooks pin to 2026.01.26 * change a word * clarifying language * Update pyproject.toml (#1813) * Update pyproject.toml * update classifiers * refactor: clean up test data handling (#1815) * import pooch_cache from conftest * remove unused files from pooch cache * move zenodo cache to conftest * remove duplicate code * min pin pooch to fix data fetching (#1820) * fix ligand network cropping bug (#1822) * fix ligand network cropping bug * move to upstream func * whitespace * fix api break check path (#1825) * fix pydantic deprecation of copy method (#1829) * fix scope mismatch with zenodo data (#1828) * fix scope mismatch with zenodo data * fix session scope --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
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
2 participants
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.
We should point users to the tutorial as the starting point, rather than the CLI api.
Blocked by OpenFreeEnergy/ExampleNotebooks#283
Checklist
newsentry, or the changes are not user-facing.pre-commit.ci autofix.Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).
Developers certificate of origin