From bb5c632d76470c8580f69fd7af5f4a7a31697360 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rok=20Ro=C5=A1kar?= Date: Thu, 11 Nov 2021 23:30:07 +0100 Subject: [PATCH 1/3] chore(docs): add spellcheck --- docs/conf.py | 1 + docs/spelling_wordlist.txt | 224 +++++++++++++++++++++++++++++++++++++ run-tests.sh | 1 + setup.py | 7 +- 4 files changed, 232 insertions(+), 1 deletion(-) create mode 100644 docs/spelling_wordlist.txt diff --git a/docs/conf.py b/docs/conf.py index cc21917991..5677348426 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -47,6 +47,7 @@ "sphinx.ext.doctest", "sphinx.ext.intersphinx", "sphinx.ext.viewcode", + "sphinxcontrib.spelling", ] # Add any paths that contain templates here, relative to this directory. diff --git a/docs/spelling_wordlist.txt b/docs/spelling_wordlist.txt new file mode 100644 index 0000000000..0b30571af5 --- /dev/null +++ b/docs/spelling_wordlist.txt @@ -0,0 +1,224 @@ +acyclic +admin +Amalthea +analytics +app +argv +attrs +auditability +auth +autocomplete +autosave +autosaved +backend +backends +backgroundImage +balancer +Bergstrom +Bioconductor +Bitnami +blog +BMP +bugfix +chartpress +Chartpress +checksum +checksums +ci +CI +circumventable +cli +CLI +conda +config +contentMd +cookiecutter +Cookiecutter +coopetition +CountFlights +cronjob +Cuda +customizable +cwl +CWL +dataset +datasets +dataverse +Dataverse +deployer +deserialize +Deserialize +discoverable +Dockerfile +dockerfiles +Dockerfiles +dockerhub +dockerignore +dotfiles +dropdown +entrypoint +executables +extraEnv +extraEnvFrom +filesystem +FilterFlights +findable +Fortran +gapped +git-lfs +github +gitignore +gitkeep +gitlab +GitLab +gitlabClientSecret +GraphQL +hostname +https +hyperkit +hypervisor +iframes +indices +Indices +init +interoperability +io +ipynb +iteratively +ize +izing +Janusgraph +Jena +JPEG +json +jsonld +jupyter +Jupyterhub +JupyterHub +jupyterlab +JupyterLab +kb +keycloak +Keycloak +ku +kubernetes +kus +lefthand +lfs +localhost +Matlab +metadata +microservices +middleware +migrationscheck +minikube +minimalistic +mistyped +mydomain +namespace +namespaces +Nginx +nodejs +oauth +OAuth +ok +online +OpenID +openssl +papermill +parameterizable +parametrize +parametrized +pipenv +PNG +Postgresql +powerline +pre +prepend +preprocessed +preprocessing +programmatically +py +pyshacl +rdflib +readme +rebase +refactor +Refactor +refactored +renku +Renku +renkulab +renv +repo +reproducibility +Reproducibility +reproducibly +reusability +Reusability +righthand +roadmap +Roadmap +rstudio +RStudio +runnable +runtime +runtimes +scala +SPARQL +spawner +SQLAlchemy +statefulset +statuspage +subclass +Subclass +subclasses +Subclasses +subdirectories +subdirectory +subgraph +Subgraph +submodule +submodules +substep +substeps +sudo +supertype +supertypes +symlink +symlinks +templated +Tensorboard +Tensorflow +timestamp +tinkerpop +toolchain +tutorialLink +txt +typesystem +Ubuntu +ui +unhandled +unicode +unlink +Unlink +unmapped +untracked +untracked +url +username +versioned +versioning +Versioning +vertices +vm +webhook +webhooks +wildcard +workflow +workflows +worktree +yaml +yml +Zenodo +連句 diff --git a/run-tests.sh b/run-tests.sh index b0104e21e2..57b9ede224 100755 --- a/run-tests.sh +++ b/run-tests.sh @@ -46,6 +46,7 @@ check_styles(){ build_docs(){ sphinx-build -qnNW docs docs/_build/html + sphinx-build -nNW -b spelling -d docs/_build/doctrees docs docs/_build/spelling pytest -v -m "not integration and not publish" -o testpaths="docs conftest.py" --ignore=docs/conf.py } diff --git a/setup.py b/setup.py index 993e7f2edb..a7143d8abd 100644 --- a/setup.py +++ b/setup.py @@ -133,7 +133,12 @@ def run(self): extras_require = { - "docs": ["Jinja2>=2.11.3,<3.0.2", "renku-sphinx-theme>=0.2.0", "sphinx-rtd-theme>=0.5.0,<1.1"], + "docs": [ + "Jinja2>=2.11.3,<3.0.2", + "renku-sphinx-theme>=0.2.0", + "sphinx-rtd-theme>=0.5.0,<1.1", + "sphinxcontrib-spelling==7.*" + ], "runner": ["cwlref-runner==1.0"], "notebook": [], "tests": tests_require, From 584e53bdf3777e231d93efc1eea4055842d6e711 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rok=20Ro=C5=A1kar?= Date: Tue, 16 Nov 2021 16:45:23 +0100 Subject: [PATCH 2/3] chore(docs): spelling --- CHANGES.rst | 74 +++++++++---------- docs/conf.py | 2 +- docs/spelling_wordlist.txt | 26 +++++++ .../management/workflow/value_resolution.py | 2 +- 4 files changed, 65 insertions(+), 39 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index e2c2b3f4a7..468035f88e 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -32,7 +32,7 @@ Bug Fixes Bug Fixes ~~~~~~~~~ -- **core:** Update to rdflib 6 and remove rdflib-jsonld which was not installable with setuptools>58.0.2 +- **core:** Update to rdflib 6 and remove rdflib-jsonld which was not installable with ``setuptools>58.0.2`` `0.16.0 `__ (2021-07-08) ---------------------------------------------------------------------------------------------------------- @@ -40,7 +40,7 @@ Bug Fixes Bug Fixes ~~~~~~~~~ -- **cli:** Fix Git LFS autocommit hook not committing new pointer files +- **cli:** Fix Git LFS auto-commit hook not committing new pointer files (`#2139 `__) (`dca5aa4 `__) - **cli:** prevent –template-ref from being set without –template-source in renku init @@ -56,7 +56,7 @@ Bug Fixes - **core:** fix CWL to work with filenames with spaces (`#2187 `__) (`634f2b3 `__), -- **core:** fix zenodo dataset import for datasets with schema:image set +- **core:** fix Zenodo dataset import for datasets with schema:image set (`#2142 `__) (`06d4969 `__) - **core:** fix duplicate project version in flattened JSON-LD @@ -137,7 +137,7 @@ Features - **core:** add default value to all Run parameters (`#2057 `__) (`3a0321d `__) -- **core:** adds node-js detection for rerun/update +- **core:** adds ``node-js`` detection for rerun/update (`#2002 `__) (`8b9e801 `__) - **core:** add renku login command to authenticate with a renku @@ -157,7 +157,7 @@ Features - **workflow:** add workflow naming metadata (`#2033 `__) (`5612199 `__) -- **service:** add delayed write operations, ie. porcelain and better cache management +- **service:** add delayed write operations, i.e. porcelain and better cache management (`#1957 `__) (`a05b615 `__) @@ -188,7 +188,7 @@ Features - **cli:** support template and docker migration (`#2019 `__) (`ed87770 `__) -- **dataset:** support moving files between datasets with renku mv +- **dataset:** support moving files between datasets with renku ``mv`` (`#1993 `__) (`a715b70 `__) @@ -221,7 +221,7 @@ Features - **dataset:** dataset import enhancements (`#1970 `__) (`b3df7b8 `__) -- **service:** renku service up/down/ps/restart/logs commands +- **service:** renku service ``up``/``down``/``ps``/``restart``/``logs`` commands (`#1899 `__) (`d9e49ae `__) - **service:** add support for storing remote dataset images in the repo @@ -351,7 +351,7 @@ Bug Fixes - **core:** adds pre-commit hook message for unsupported projects (`#1730 `__) (`7f1731d `__) -- **service:** removes chdir calls in service +- **service:** removes ``chdir`` calls in service (`#1767 `__) (`4da22cb `__) @@ -456,7 +456,7 @@ Bug Fixes - **dataset:** remove blank nodes (`#1602 `__) (`478f08c `__) -- **dataset:** set isBasedOn for renku datasets +- **dataset:** set ``isBasedOn`` for renku datasets (`#1617 `__) (`3aee6b8 `__) - **dataset:** update local files metadata when overwriting @@ -465,7 +465,7 @@ Bug Fixes - **dataset:** various migration issues (`#1620 `__) (`f24c2e4 `__) -- **service:** correctely set job timeout +- **service:** correctly set job timeout (`#1677 `__) (`25f0eb6 `__) - **service:** dataset rm endpoint supports new core API @@ -484,7 +484,7 @@ Features - **cli:** add click plugin support (`#1604 `__) (`47b007f `__) -- **cli:** adds consistent behaviour for cli commands +- **cli:** adds consistent behavior for cli commands (`#1523 `__) (`20b7248 `__) - **cli:** show lfs status of dataset files @@ -499,7 +499,7 @@ Features - **dataset:** list dataset description (`#1588 `__) (`7e13857 `__) -- **service:** adds template and dockerfile migration to migration +- **service:** adds template and Dockerfile migration to migration endpoint (`#1509 `__) (`ea01795 `__) @@ -573,10 +573,10 @@ Bug Fixes Bug Fixes ~~~~~~~~~ -- **cli:** fixes libxslt dependency in docker image +- **cli:** fixes ``libxslt`` dependency in docker image (`#1534 `__) (`491bae7 `__) -- **core:** fixes ‘doi:…’ import +- **core:** fixes ``doi:…`` import (`#1536 `__) (`f653c79 `__) - **core:** fixes duplicate ‘renku:Run’ ids on repeat execution of migrations @@ -618,7 +618,7 @@ Features Bug Fixes ~~~~~~~~~ -- fixes shacl for DatasetFile when used inside a qualifiedGeneration +- fixes shacl for DatasetFile when used inside a ``qualifiedGeneration`` (`#1477 `__) (`99dd4a4 `__) @@ -628,7 +628,7 @@ Bug Fixes Bug Fixes ~~~~~~~~~ -- **cli:** disable version check in githook calls +- **cli:** disable version check in git hook calls (`#1300 `__) (`5132db3 `__) - **core:** fix paths in migration of workflows @@ -679,7 +679,7 @@ Features - **core:** migration check in core (`#1320 `__) (`4bc52f4 `__) -- **core:** Move workflow serialisation over to calamus +- **core:** Move workflow serialization over to calamus (`#1386 `__) (`f0fbc49 `__) - **core:** save and load workflow as jsonld @@ -739,7 +739,7 @@ Bug Fixes Bug Fixes ~~~~~~~~~ -- **dataset:** update default behaviour and messaging on dataset unlink +- **dataset:** update default behavior and messaging on dataset unlink (`#1275 `__) (`98d6728 `__) - **dataset:** correct url in different domain @@ -773,7 +773,7 @@ Features - **service:** protected branches support (`#1222 `__) (`8405ce5 `__) -- **dataset:** doi variations for import +- **dataset:** DOI variations for import (`#1216 `__) (`0f329dd `__) - **dataset:** keywords in metadata @@ -853,7 +853,7 @@ Features - renku init options refactor (`#1127 `__) (`78b208b `__) -- **datasets:** add files from dropbox +- **datasets:** add files from Dropbox (`#1135 `__) (`bf5f2db `__) @@ -881,7 +881,7 @@ will insist on migrating a project immediately if the metadata is found to be ou Bug Fixes ~~~~~~~~~ -- **cli:** consistenly show correct contexts +- **cli:** consistently show correct contexts (`#1096 `__) (`b333f0f `__) - **dataset:** –no-external-storage flag not working @@ -1023,7 +1023,7 @@ Bug Fixes - Fixes renku update workflow failure handling and renku status error handling (`#888 `__) (`3879124 `__) -- Fixes sameAs property to follow schema.org spec +- Fixes ``sameAs`` property to follow schema.org spec (`#944 `__) (`291380e `__) - handle missing renku directory @@ -1032,7 +1032,7 @@ Bug Fixes - resolves symlinks when pulling LFS (`#981 `__) (`68bd8f5 `__) -- serializes all zenodo metadata +- serializes all Zenodo metadata (`#941 `__) (`787978a `__) - Fixes various bugs in dataset import @@ -1153,7 +1153,7 @@ Bug Fixes Bug Fixes ~~~~~~~~~ -- add .renku/tmp to default .gitignore (`#728`_) (`6212148`_) +- add ``.renku/tmp`` to default .gitignore (`#728`_) (`6212148`_) - dataset import causes renku exception due to duplicate LocalClient (`#724`_) (`89411b0`_) - delete new dataset ref if file add fails (`#729`_) (`2dea711`_) @@ -1163,7 +1163,7 @@ Bug Fixes - integration tests for `#681`_ (`#747`_) (`b08435d`_) - use commit author for project creator (`#715`_) (`1a40ebe`_), closes `#713`_ -- zenodo dataset import error (`f1d623a`_) +- Zenodo dataset import error (`f1d623a`_) Features ~~~~~~~~ @@ -1218,13 +1218,13 @@ Bug Fixes - cleanup needed for integration tests on py35 (`#653 `__) (`fdd7215 `__) -- fixed serialization of datetime to iso format +- fixed serialization of datetime to ISO format (`#629 `__) (`693d59d `__) - fixes broken integration test (`#649 `__) (`04eba66 `__) -- hide image, pull, runner, show, workon and deactivate commands +- hide ``image``, ``pull``, ``runner``, ``show``, ``workon`` and ``deactivate`` commands (`#672 `__) (`a3e9998 `__) - integration tests fixed @@ -1233,10 +1233,10 @@ Bug Fixes - migration of old datasets (`#639 `__) (`4d4d7d2 `__) -- migration timezones +- migration time zones (`#683 `__) (`58c2de4 `__) -- Removes unneccesary call to git lfs with no paths +- Removes unnecessary call to git lfs with no paths (`#658 `__) (`e32d48b `__) - renku home directory overwrite in tests @@ -1245,7 +1245,7 @@ Bug Fixes - upload metadata before actual files (`#652 `__) (`95ed468 `__) -- use latest_html for version check +- use ``latest_html`` for version check (`#647 `__) (`c6b0309 `__), closes @@ -1253,7 +1253,7 @@ Bug Fixes - user-related metadata (`#655 `__) (`44183e6 `__) -- zenodo export failing with relative paths +- Zenodo export failing with relative paths (`d40967c `__) Features @@ -1317,7 +1317,7 @@ Bug Fixes - added check for overwriting datasets (`#541 `__) (`8c697fb `__) -- escape whitespaces in notebook name +- escape whitespace in notebook name (`#584 `__) (`0542fcc `__) - modify json-ld for datasets @@ -1326,7 +1326,7 @@ Bug Fixes closes `#525 `__ `#526 `__ -- refactored tests and docs to align with updated pydoctstyle +- refactored tests and docs to align with updated ``pydocstyle`` (`#586 `__) (`6f981c8 `__) - **cli:** add check of missing references @@ -1365,7 +1365,7 @@ Features - add dataset metadata to the KG (`#558 `__) (`fb443d7 `__) -- **datasets:** export dataset to zenodo +- **datasets:** export dataset to Zenodo (`#529 `__) (`fc6fd4f `__) - added support for working on dirty repo @@ -1373,13 +1373,13 @@ Features - **datasets:** edit dataset metadata (`#549 `__) (`db39083 `__) -- integrate metadata from zenodo +- integrate metadata from Zenodo (`#545 `__) (`4273d2a `__) - **config:** added global config manager (`#533 `__) (`938f820 `__) -- **datasets:** import data from zenodo +- **datasets:** import data from Zenodo (`#509 `__) (`52b2769 `__) @@ -1428,7 +1428,7 @@ Features (`c755d7b `__), closes `#426 `__ -- generate Makefile with log –format Makefile +- generate ``Makefile`` with ``log –format Makefile`` (`1e440ce `__) ``v0.4.0`` diff --git a/docs/conf.py b/docs/conf.py index 5677348426..5401e8773e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -96,7 +96,7 @@ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ["_build"] +exclude_patterns = ["_build", "CHANGES.rst"] # The reST default role (used for this markup: `text`) to use for all # documents. diff --git a/docs/spelling_wordlist.txt b/docs/spelling_wordlist.txt index 0b30571af5..0454d6fd97 100644 --- a/docs/spelling_wordlist.txt +++ b/docs/spelling_wordlist.txt @@ -2,8 +2,11 @@ acyclic admin Amalthea analytics +api app +args argv +async attrs auditability auth @@ -20,6 +23,7 @@ Bitnami blog BMP bugfix +Calamus chartpress Chartpress checksum @@ -46,6 +50,7 @@ datasets dataverse Dataverse deployer +deserialization deserialize Deserialize discoverable @@ -55,6 +60,7 @@ Dockerfiles dockerhub dockerignore dotfiles +Dropbox dropdown entrypoint executables @@ -73,6 +79,7 @@ gitlab GitLab gitlabClientSecret GraphQL +Homebrew hostname https hyperkit @@ -81,6 +88,7 @@ iframes indices Indices init +installable interoperability io ipynb @@ -103,6 +111,7 @@ Keycloak ku kubernetes kus +ld lefthand lfs localhost @@ -121,6 +130,7 @@ Nginx nodejs oauth OAuth +oid ok online OpenID @@ -143,9 +153,11 @@ pyshacl rdflib readme rebase +redirections refactor Refactor refactored +Renga renku Renku renkulab @@ -154,6 +166,7 @@ repo reproducibility Reproducibility reproducibly +resync reusability Reusability righthand @@ -165,21 +178,27 @@ runnable runtime runtimes scala +shacl SPARQL spawner SQLAlchemy statefulset statuspage +stderr +stdin +stdout subclass Subclass subclasses Subclasses +subcommand subdirectories subdirectory subgraph Subgraph submodule submodules +subpath substep substeps sudo @@ -202,11 +221,13 @@ unhandled unicode unlink Unlink +unlinking unmapped untracked untracked url username +validator versioned versioning Versioning @@ -214,10 +235,15 @@ vertices vm webhook webhooks +whitespace wildcard workflow +Workflow workflows +Workflows worktree +worktree +worktrees yaml yml Zenodo diff --git a/renku/core/management/workflow/value_resolution.py b/renku/core/management/workflow/value_resolution.py index cf481ed377..fd5e08447b 100644 --- a/renku/core/management/workflow/value_resolution.py +++ b/renku/core/management/workflow/value_resolution.py @@ -15,7 +15,7 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. -"""Resolution of Worklow execution values precedence.""" +"""Resolution of ``Workflow`` execution values precedence.""" from abc import ABC, abstractmethod from itertools import chain From a190b5397a4ece996adc10027c6f569095d5108c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rok=20Ro=C5=A1kar?= Date: Wed, 17 Nov 2021 11:17:23 +0100 Subject: [PATCH 3/3] parametrize not parameterererererize! --- docs/spelling_wordlist.txt | 1 + renku/cli/workflow.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/spelling_wordlist.txt b/docs/spelling_wordlist.txt index 0454d6fd97..74df78b1c7 100644 --- a/docs/spelling_wordlist.txt +++ b/docs/spelling_wordlist.txt @@ -137,6 +137,7 @@ OpenID openssl papermill parameterizable +parametrization parametrize parametrized pipenv diff --git a/renku/cli/workflow.py b/renku/cli/workflow.py index a5b260f5a5..68de523e31 100644 --- a/renku/cli/workflow.py +++ b/renku/cli/workflow.py @@ -118,7 +118,7 @@ :width: 850 :alt: Iterate Plans -For executing a Plan with different parameterization ``renku workflow iterate`` +For executing a Plan with different parametrization ``renku workflow iterate`` could be used. This sub-command is basically conducting a 'grid search'-like execution of a Plan, with parameter-sets provided by the user.