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2023-05-22Enable running application under pdb.Frederick Muriuki Muriithi
Add an option to help with running the application under pdb, and add some documentation to help other developers figure it out.
2022-12-29README: Update invocation command for pytestFrederick Muriuki Muriithi
Invoke pytest via python so as to ensure that all the relevant modules are found when running tests.
2022-11-16Add SPARQL_ENDPOINT in examples in READMEMunyoki Kilyungi
2022-09-08Recommend pytests in READMEMunyoki Kilyungi
* README.md (Testing): Using pytests instead of unittests.
2022-09-06Update link to continuous deployment.Arun Isaac
* README.md (Development): Update link to continuous deployment.
2022-08-12Add a profiling scriptFrederick Muriuki Muriithi
Add a script to enable profiling the code.
2022-05-05Link to continuous deployment in README.Arun Isaac
* README.md (Development): Link to continuous deployment.
2022-03-21Fix command in documentationFrederick Muriuki Muriithi
Add missing argument to the command in the documentation
2022-03-18README: Update CI badge subdomain.Arun Isaac
The CI has been migrated from penguin2.genenetwork.org to ci.genenetwork.org. * README.md: Update CI badge subdomain.
2022-03-18Document configurationsFrederick Muriuki Muriithi
Document the configurations for the service, and how to use them when invoking the service.
2022-03-17Document how to run testsFrederick Muriuki Muriithi
Add documentation on how to run the tests - this was no clear from the existing documentation up to this point.
2022-02-18README: Replace GitHub actions badge with Laminar CI badge.Arun Isaac
* README.md: Replace GitHub actions badge with Laminar CI badge.
2022-01-28Revert "bin: Set GN2_PROFILE from GUIX_ENVIRONMENT."Arun Isaac
This reverts commit f4e336eb1ea526156e112cff97a3ec8137a2bc90.
2022-01-28Revert "bin: Do not set environment variables set by guix shell."Arun Isaac
This reverts commit 344e428126b60932bff4c62c5ded8c36519155e8.
2022-01-28Revert "README: Document `guix shell' development process."Arun Isaac
This reverts commit e0a260b0de55fbea0c507eb0ca5fbdc3c1a825c0.
2022-01-06README: Document `guix shell' development process.Arun Isaac
* README.md: Clean up and document `guix shell' development process.
2022-01-06README: Fix typo.Arun Isaac
* README.md: Change clinians to clinicians.
2022-01-06bin: Do not set environment variables set by guix shell.Arun Isaac
The Guix python package accepts GUIX_PYTHONPATH instead of PYTHONPATH. `guix shell' sets GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, GUIX_PYTHONPATH, PATH, R_LIB_SITE and XDG_DATA_DIRS when necessary. There is no need to set these environment variables explicitly. * bin/genenetwork2: Do not set GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, PATH, PYTHONPATH, R_LIBS_SITE and XDG_DATA_DIRS. * README.md [Development]: Remove paragraph on injecting python modules locally.
2022-01-06bin: Set GN2_PROFILE from GUIX_ENVIRONMENT.Arun Isaac
`guix shell' sets the profile path in an environment variable---GUIX_ENVIRONMENT. There is no need to pass it explicity as an input in GN2_PROFILE. * README.md: Remove all references to GN2_PROFILE. * bin/genenetwork2: Set GN2_PROFILE from GUIX_ENVIRONMENT. Do not check the value of GN2_PROFILE now that it is set automatically. Remove all references to GN2_PROFILE in example invocations.
2021-12-01Figure out that we are using the wrong db_webqtl_s!Pjotr Prins
2021-12-01Introduce GN3_PYTHONPATH environment variablePjotr Prins
2021-10-28README.md: Add GN_PROXY_URL and GN3_LOCAL_URL to documentationBonfaceKilz
2021-08-24README: minor editsPjotr Prins
2021-01-13Just some tweaks to first paragrfaphrobwwilliams
2020-09-22Add testing badge on READMEBonfaceKilz
* README.md: Badge becomes green on successful runs.
2020-09-22Update documentation on testing and CIBonfaceKilz
* README.md: Update section on testing. * doc/docker-container.org: Add it.
2020-07-27Merge branch 'testing' into testingPjotr Prins
2020-07-26Document how to run testsBonfaceKilz
* README.md: - Add details on how to run unit tests - Update link that points to Mechanical Rob
2020-07-25Updating docs and show how to include a local Python modulePjotr Prins
2020-04-26Merge master and testingmasterPjotr Prins
2019-02-18typoPjotr Prins
2019-02-18Note on running testsPjotr Prins
2018-09-05ELASTICSEARCH settings and fix runserver.py to run without gunicornPjotr Prins
2018-04-16Docs on elasticsearch usePjotr Prins
2018-04-12README and docsPjotr Prins
2016-06-14Adding documentationPjotr Prins
2016-06-14Add JOSS citationPjotr Prins
2016-06-14Add JOSS citationPjotr Prins
2016-06-09README: capitalizationPjotr Prins
2016-06-02Paper: addressing JOSS requirements for contribution, where to findPjotr Prins
documentation and testing materials https://github.com/openjournals/joss-reviews/issues/25
2016-05-29Updated webserver linkPjotr Prins
2016-05-29CitationPjotr Prins
2016-05-29Add zenodo doiPjotr Prins
2016-04-20README: point to gn-latest SHA valuesPjotr Prins
2016-04-20Main READMEPjotr Prins
2016-04-20READMEPjotr Prins
2016-04-20READMEPjotr Prins
2016-04-20READMEPjotr Prins
2016-04-20Simplify the README so people can actually READ it.Pjotr Prins
2016-04-20[PATCH 023/100] WIP fixing all pathsPjotr Prins
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