Rework API documentation #156
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chStaiger
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API: - Move data objects and collections, aka rename - Improve connection checks - Rework the API - Bugfix in search - Examples in docstrings CLI: - Adding mkcoll and tree Update tutorials * Adding mkdir to CLI (#137) * Adding mkdir to CLI * pylint * Update ibridges/__main__.py Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> * Update ibridges/__main__.py Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> * Update ibridges/__main__.py Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> * Rename to mkcoll --------- Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> * Move data objects and collections (#136) * Adding moveing data objects and collections * Adding test for renaming * Renaming and adjusting tests. * Create dependabot.yml (#143) * Check for host and port before checking network (#139) * Check for host and port before checking network * Small changes --------- Co-authored-by: Staiger, Christine <christine.staiger@wur.nl> * Update sphinx requirement from <7.0.0 to <8.0.0 (#145) * Adding IrodsPath doc * Small changes and index * Turning network_check into class method for GUI (#146) * Turning network_check into class method for GUI * Ruff * Install doc (#147) * Create install.rst * Adding install instructions * Update docs/source/install.rst Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> * Update docs/source/install.rst Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> --------- Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> * Fix docstring formatting error (#140) * Fix docstring formatting error * Add ruff to CI and fix small linting errors * Add sync documentation. (#148) * Add sync documentation. * add index * Update docs/source/sync.rst Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> * FOrmatting and small changes * Ruff --------- Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> Co-authored-by: Staiger, Christine <christine.staiger@wur.nl> * Ipath doc (#153) * Update ipath with other documentation (#152) * Turning network_check into class method for GUI (#146) * Turning network_check into class method for GUI * Ruff * Install doc (#147) * Create install.rst * Adding install instructions * Update docs/source/install.rst Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> * Update docs/source/install.rst Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> --------- Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> * Fix docstring formatting error (#140) * Fix docstring formatting error * Add ruff to CI and fix small linting errors * Add sync documentation. (#148) * Add sync documentation. * add index * Update docs/source/sync.rst Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> * FOrmatting and small changes * Ruff --------- Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> Co-authored-by: Staiger, Christine <christine.staiger@wur.nl> --------- Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> Co-authored-by: Staiger, Christine <christine.staiger@wur.nl> * Formatting and cross referencing. --------- Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> Co-authored-by: Staiger, Christine <christine.staiger@wur.nl> * Update ipath.rst * Update ipath.rst * Move functions to utils and add walk to IrodsPath (#151) * Add missing search for data_name (#161) * Add missing search for data_name * Rework API documentation (#156) * Rework API documentation * TRying to add file to resolve conflict * Rremove added file * Adding to edit * Delete file again. --------- Co-authored-by: chstaiger <staigerchristine@gmail.com> Co-authored-by: chStaiger <c.staiger@uu.nl> * Bugfix in search (#162) * Don't use assert for control flow (#166) * Don't use assert for control flow * Fix __main__.py Only throw exception when needed. * Update ibridges/path.py Co-authored-by: chStaiger <c.staiger@uu.nl> --------- Co-authored-by: chStaiger <c.staiger@uu.nl> * Update iRODS path tutorial. (#165) * Update iRODS path tutorial. * Refer to tutorials for iRODS paths in RTD * Some more hints on paths in cli doc * Adjustong README * Remove old tutorial * Small edits * Update docs/source/cli.rst Co-authored-by: Terrell Russell <terrellrussell@gmail.com> --------- Co-authored-by: Terrell Russell <terrellrussell@gmail.com> * Sync update (#158) Rewrite of the sync_data function so that it uses the walk functionality of the IrodsPath instead of duplicated effort. Performance should be roughly the same. This update also fixes some issues with the walk functionality of the IrodsPath and makes it much faster. * Add tree for the iBridges CLI (#159) * Add tree for the iBridges CLI * Add options to tree - Ascii - depth - show-max * Make pylint happy * Add type annotations * Fix spelling errors in the README (#171) * Rewrite download/upload (#169) The main goal is code reduction and using the similarities of the download/upload and sync functionality. As a direct benefit, the upload and download functions now also have a progress bar. Some other notable changes: - `--dry-run` for upload and download - IrodsPath.absolute_path becomes IrodsPath.absolute * Cleanup tutorials. Create a First steps tutorial for the impatient. (#174) * Cleanup tutorials. Create a First steps tutorial for the impatient. * Review First steps * Update Irods-paths tutorial * Update working-with-data * Remove duplicate file --------- Co-authored-by: Raoul Schram <r.d.schram@uu.nl> * update metadata * Fix behavior of parent property of IrodsPath (#175) * Fix behavior of parent property of IrodsPath * Fix the fix * Fix tests for new behavior * Fix tutorials (#177) * Spellchecking tutorials * Turn None time into empty string in listing tickets. (#178) * Add examples (#180) Add examples to many of the mostly used docstrings. Also contains a few tiny fixes. * Ruff --------- Co-authored-by: qubixes <44498096+qubixes@users.noreply.github.com> Co-authored-by: Dawa Ometto <d.ometto@gmail.com> Co-authored-by: Staiger, Christine <christine.staiger@wur.nl> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Terrell Russell <terrellrussell@gmail.com> Co-authored-by: Raoul Schram <r.d.schram@uu.nl>
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