-
Notifications
You must be signed in to change notification settings - Fork 26
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
[FDS-2449] Lock sphinx
version and update poetry.lock
#1530
Conversation
This should fix this trivy issue: #1531 |
2b94cdc
to
3d1fecb
Compare
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Thanks for the update!
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Do you have to change the installation instructions in .readthedocs.yml
for this to work? This worked for me , but im not sure that's the right approach (maybe it is for the short term)
poetry install --all-extras
I'm getting
Running Sphinx v7.3.7
loading translations [English]... not available for built-in messages
making output directory... done
WARNING: html_static_path entry '_static' does not exist
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 2 source files that are out of date
updating environment: [new config] 2 added, 0 changed, 0 removed
reading sources... [100%] index
/Users/tyu/sage/schematic/docs/source/cli_reference.rst:5: ERROR: Failed to import "main" from "schematic.__main__". The following exception was raised:
Traceback (most recent call last):
File "/Users/tyu/anaconda3/envs/schematic/lib/python3.10/site-packages/sphinx_click/ext.py", line 403, in _load_module
mod = __import__(module_name, globals(), locals(), [attr_name])
File "/Users/tyu/sage/schematic/schematic/__init__.py", line 8, in <module>
from opentelemetry.instrumentation.flask import FlaskInstrumentor
ModuleNotFoundError: No module named 'opentelemetry.instrumentation.flask'
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... copying static files... done
copying extra files... done
done
writing output... [100%] index
generating indices... genindex done
writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 2 warnings.
The HTML pages are in _build/html.
I added a deployment here: https://schematicpy.readthedocs.io/en/fds-2449-fix-rtd/cli_reference.html. which will auto build your branch when you make changes
No, I changed it so I'd have the opportunity to explain the groups being downloaded with the command. I thought this would be better than doing an |
@jaymedina Makes sense, lets confirm that this builds: https://schematicpy.readthedocs.io/en/fds-2449-fix-rtd/cli_reference.html. You can log into readthedocs to view the schematicpy builds and logs. We may want to add dependencies then to the |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
🔥 LGTM!
@jaymedina Can you make sure the tests run locally? My concern is that there are dependency version updates, so the 3.10 tests not passing is unfortunate.. Otherwise, I approve of this! The tests passed (i just re-ran them) |
|
Also install `typing-extensions` in the build
* add new tests * add unit tests * ran black * Update schematic/models/validate_attribute.py Co-authored-by: BryanFauble <17128019+BryanFauble@users.noreply.github.com> * added tests * Update README.md * Update README.md * add unit tests * run black * Update README.md * temp commit * remove old tests * [FDS-2386] Synapse entity tracking and code concurrency updates (#1505) * [FDS-2386] Synapse entity tracking and code concurrency updates * ran black * Update CODEOWNERS * updated data model type rules to include error param * fix validate type attribute to use msg level param * added error handling * run black * create Node class * sat up Node class so that nodes with no displayName fields cause an error on creation * ran black * ran mypy * added new configs for CLI tests * added new manifests for testing CLI commands * automate manual CLI tests * ran black * Update CODEOWNERS * Update scan_repo.yml * Update .github/CODEOWNERS * Update .github/workflows/scan_repo.yml * Attach additional telemetry data to OTEL traces (#1519) * Attach additional telemetry data to OTEL traces * feat: added tracing for cross manifest validation and file name validation (#1509) * add tracing for GX validation * temp commit * Updating contribution doc to expect squash and merge (#1534) * [FDS-2491] Integration tests for Schematic API Test plan (#1512) Integration tests for Schematic API Test plan * [FDS-2500] Add Integration Tests for: Manifest Validation (#1516) * Add Integration Tests for: Manifest Validation * [FDS-2449] Lock `sphinx` version and update `poetry.lock` (#1530) Also install `typing-extensions` in the build * manual test files now being saved in manifests folder * manual test files now being saved in manifests folder * remove lines to delete json files that were under git control * ran black * add try finally blocks to remove created files * ran black * add lines to remove created json files * Update file annotation store process to require filename be present in order to annotate file * add lines to remove created json files * Revert "Update file annotation store process to require filename be present in order to annotate file" This reverts commit f57c718. * Don't attempt to annotate the table * add code in finally blocks to reset config to default values, when tests change them * complete submit manifest command test * ran black * add test for bug case * update test for table tidyness * remove unused import * remove etag column if already present when building temp file view * catch all exceptions to switch to sequential mode * update test for updated data * Revert "update test for updated data" This reverts commit 255e3c0. * Revert "catch all exceptions to switch to sequential mode" This reverts commit 68b0b24. * catch ValueErrors as well * Updates for integration test failures (#1537) * Updates for integration test failures, Config file reset and scope changes * add todos for removing config resets * [FDS-2525] Authenticated export of telemetry data (#1527) * Authenticated export of telemetry data, updating to HTTP otel library * temp reduce tests * restore tests * uncomment tests * redid how files are deleted, manual tests values are set * ran black * [SCHEMATIC-157] Make some dependencies required to avoid `schematic CLI` commands from potentially erroring when doing a pip install (#1540) * Make otel flash non-optional * Add dependencies as non-optional * Update pyproject.toml --------- Co-authored-by: BryanFauble <17128019+BryanFauble@users.noreply.github.com> Co-authored-by: Jenny V Medina <jenny.medina@sagebase.org> Co-authored-by: Thomas Yu <thomas.yu@sagebase.org> Co-authored-by: Lingling <55448354+linglp@users.noreply.github.com> Co-authored-by: GiaJordan <gianna.jordan@sagebase.org>
* add new tests * add unit tests * ran black * Update schematic/models/validate_attribute.py Co-authored-by: BryanFauble <17128019+BryanFauble@users.noreply.github.com> * added tests * Update README.md * Update README.md * add unit tests * run black * Update README.md * temp commit * remove old tests * [FDS-2386] Synapse entity tracking and code concurrency updates (#1505) * [FDS-2386] Synapse entity tracking and code concurrency updates * ran black * Update CODEOWNERS * updated data model type rules to include error param * fix validate type attribute to use msg level param * added error handling * run black * create Node class * sat up Node class so that nodes with no displayName fields cause an error on creation * ran black * ran mypy * added new configs for CLI tests * added new manifests for testing CLI commands * automate manual CLI tests * ran black * Update CODEOWNERS * Update scan_repo.yml * Update .github/CODEOWNERS * Update .github/workflows/scan_repo.yml * Attach additional telemetry data to OTEL traces (#1519) * Attach additional telemetry data to OTEL traces * feat: added tracing for cross manifest validation and file name validation (#1509) * add tracing for GX validation * temp commit * Updating contribution doc to expect squash and merge (#1534) * [FDS-2491] Integration tests for Schematic API Test plan (#1512) Integration tests for Schematic API Test plan * [FDS-2500] Add Integration Tests for: Manifest Validation (#1516) * Add Integration Tests for: Manifest Validation * [FDS-2449] Lock `sphinx` version and update `poetry.lock` (#1530) Also install `typing-extensions` in the build * manual test files now being saved in manifests folder * manual test files now being saved in manifests folder * remove lines to delete json files that were under git control * ran black * add try finally blocks to remove created files * ran black * add lines to remove created json files * Update file annotation store process to require filename be present in order to annotate file * add lines to remove created json files * Revert "Update file annotation store process to require filename be present in order to annotate file" This reverts commit f57c718. * Don't attempt to annotate the table * add code in finally blocks to reset config to default values, when tests change them * complete submit manifest command test * ran black * add test for bug case * update test for table tidyness * remove unused import * remove etag column if already present when building temp file view * catch all exceptions to switch to sequential mode * update test for updated data * Revert "update test for updated data" This reverts commit 255e3c0. * Revert "catch all exceptions to switch to sequential mode" This reverts commit 68b0b24. * catch ValueErrors as well * Updates for integration test failures (#1537) * Updates for integration test failures, Config file reset and scope changes * add todos for removing config resets * [FDS-2525] Authenticated export of telemetry data (#1527) * Authenticated export of telemetry data, updating to HTTP otel library * temp reduce tests * restore tests * uncomment tests * redid how files are deleted, manual tests values are set * ran black * [SCHEMATIC-157] Make some dependencies required to avoid `schematic CLI` commands from potentially erroring when doing a pip install (#1540) * Make otel flash non-optional * Add dependencies as non-optional * Include schematic_api for now (#1547) * update toml version to 24.11.1 --------- Co-authored-by: BryanFauble <17128019+BryanFauble@users.noreply.github.com> Co-authored-by: Jenny V Medina <jenny.medina@sagebase.org> Co-authored-by: Thomas Yu <thomas.yu@sagebase.org> Co-authored-by: Lingling <55448354+linglp@users.noreply.github.com> Co-authored-by: GiaJordan <gianna.jordan@sagebase.org>
* add new tests * add unit tests * ran black * Update schematic/models/validate_attribute.py Co-authored-by: BryanFauble <17128019+BryanFauble@users.noreply.github.com> * added tests * Update README.md * Update README.md * add unit tests * run black * Update README.md * temp commit * remove old tests * [FDS-2386] Synapse entity tracking and code concurrency updates (#1505) * [FDS-2386] Synapse entity tracking and code concurrency updates * ran black * Update CODEOWNERS * updated data model type rules to include error param * fix validate type attribute to use msg level param * added error handling * run black * create Node class * sat up Node class so that nodes with no displayName fields cause an error on creation * ran black * ran mypy * added new configs for CLI tests * added new manifests for testing CLI commands * automate manual CLI tests * ran black * Update CODEOWNERS * Update scan_repo.yml * Update .github/CODEOWNERS * Update .github/workflows/scan_repo.yml * Attach additional telemetry data to OTEL traces (#1519) * Attach additional telemetry data to OTEL traces * feat: added tracing for cross manifest validation and file name validation (#1509) * add tracing for GX validation * temp commit * Updating contribution doc to expect squash and merge (#1534) * [FDS-2491] Integration tests for Schematic API Test plan (#1512) Integration tests for Schematic API Test plan * [FDS-2500] Add Integration Tests for: Manifest Validation (#1516) * Add Integration Tests for: Manifest Validation * [FDS-2449] Lock `sphinx` version and update `poetry.lock` (#1530) Also install `typing-extensions` in the build * manual test files now being saved in manifests folder * manual test files now being saved in manifests folder * remove lines to delete json files that were under git control * ran black * add try finally blocks to remove created files * ran black * add lines to remove created json files * Update file annotation store process to require filename be present in order to annotate file * add lines to remove created json files * Revert "Update file annotation store process to require filename be present in order to annotate file" This reverts commit f57c718. * Don't attempt to annotate the table * add code in finally blocks to reset config to default values, when tests change them * complete submit manifest command test * ran black * add test for bug case * update test for table tidyness * remove unused import * remove etag column if already present when building temp file view * catch all exceptions to switch to sequential mode * update test for updated data * Revert "update test for updated data" This reverts commit 255e3c0. * Revert "catch all exceptions to switch to sequential mode" This reverts commit 68b0b24. * catch ValueErrors as well * Updates for integration test failures (#1537) * Updates for integration test failures, Config file reset and scope changes * add todos for removing config resets * [FDS-2525] Authenticated export of telemetry data (#1527) * Authenticated export of telemetry data, updating to HTTP otel library * temp reduce tests * restore tests * uncomment tests * redid how files are deleted, manual tests values are set * ran black * [SCHEMATIC-157] Make some dependencies required to avoid `schematic CLI` commands from potentially erroring when doing a pip install (#1540) * Make otel flash non-optional * Add dependencies as non-optional * Include schematic_api for now (#1547) * update toml version to 24.11.1 (#1548) * [SCHEMATIC-193] Support exporting telemetry data from GH integration test runs (#1550) * Support exporting telemetry data from GH run via access token retrieved via oauth2 * [SCHEMATIC-30, SCHEMATIC-200] Add version to click cli / use pathlib.Path module for checking cache size (#1542) * Add version to click cli * Add version * Run black * Reformat * Fix * Update schematic/schemas/data_model_parser.py * Add test for check_synapse_cache_size * Reformat * Fix tests * Remove unused parameter * Install all-extras for now * Make otel flash non-optional * Update dockerfile * Add dependencies as non-optional * Update pyproject toml * Fix trivy issue * Add service version * Run black * Move all utils.general tests into separate folder * Use pre-commit * Add updates to contribution doc * Fix * Add service version to log provider --------- Co-authored-by: BryanFauble <17128019+BryanFauble@users.noreply.github.com> * [SCHEMATIC-212] Prevent traces from being combined (#1552) * Set instance id in github CI run, uninstrument flask auto during integration test run * [SCHEMATIC-163] Catch error when manifest is generated and existing one doesn't have `entityId` (#1551) * adds error handling * adds unit tests for _get_file_entityIds * updates error message * adds entityid check to parent func * updates docstring * [SCHEMATIC-183] Use paths from file view for manifest generation (#1529) source manifest file paths from synapse fileviews at generation * [SCHEMATIC-214] Wrap pandas functions to support not including `None` with the NA values argument (#1553) * Wrap pandas functions to support not including `None` with the NA values argument * Ignore types * pylint issues * ordering of ignore * Add to integration test to cover none in a manifest * Add additional test for manifest * [SCHEMATIC-210] Add attribute to nones data model (#1555) Update example_test_nones.model.csv component and add new invalid manifest with nones * first commit * ran black * add test for validateModelManifest * [SCHEMATIC-214] change data model and component (#1556) * add valid values to Patient attributes * update data model * add test manifests * update test for new model * update test for new valid value * change test to use new manifests * remove uneeded test file * revert file * revert file * change tests to use new manifests * remove uneeded manifests * ran black * add tests back in * ran black * revert manifest * Split up valid and errored test as separate testing functions * Remove unused import --------- Co-authored-by: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Co-authored-by: Andrew Lamb <andrewelamb@gmail.com> Co-authored-by: Thomas Yu <thomas.yu@sagebase.org> * incremented packge version number * Update publish.yml * Update test.yml * Update api_test.yml * Update pdoc.yml * Update version.py * updates publish.yml (#1558) (#1561) Co-authored-by: Brad Macdonald <52762200+BWMac@users.noreply.github.com> --------- Co-authored-by: BryanFauble <17128019+BryanFauble@users.noreply.github.com> Co-authored-by: Jenny V Medina <jenny.medina@sagebase.org> Co-authored-by: Thomas Yu <thomas.yu@sagebase.org> Co-authored-by: Lingling <55448354+linglp@users.noreply.github.com> Co-authored-by: GiaJordan <gianna.jordan@sagebase.org> Co-authored-by: Brad Macdonald <52762200+BWMac@users.noreply.github.com> Co-authored-by: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com>
problem
The ReadTheDocs page for
schematic
was not rendering its contents properly. I was able to re-create the error when starting a new environment from scratch withsphinx
v7.4.7. I found that there was no version locked forsphinx
which led to thepoetry.lock
file updating with v7.4.7. This version caused the issue with the documentation build. While the reason isn't clear, I suspect it has something to do with v7.4.7 not working with v4.4.0 ofsphinx-click
.solution
sphinx
version in thepyproject.toml
file, which is used to create thepoetry.lock
file4.4.0
version ofsphinx-click
in thepyproject.toml
since we know that works with the new specified version ofsphinx
. This is the package that theci_references.rtd
needs in order to render properly.testing
Creating a fresh environment with the new
poetry.lock
file and building the docs locally now results in a properly rendered CLI Reference page.Here are the steps to build the docs locally off these changes:
schematic
repository while checked into this branch)Result: