Code

merge from develop#26

Code

Merged

mjkw31 merged 142 commits intomainwtsi-hgi/softpack-core:mainfrom developwtsi-hgi/softpack-core:developCopy head branch name to clipboardSep 26, 2023

+2,728-190

Commits

Commits on Jul 4, 2023

• 🐛 fix(artifacts.py): remove unused import and unused code related to Credentials model

  Show description for 0ca722e
  altaf-ali

  committed
  0ca722e

Commits on Jul 7, 2023

• skeleton code for environment mutations

  

  SamO135

  authored and

  altaf-ali

  committed
  423ee7b

• send build request to softpack-builder

  Show description for 410c203
  

  SamO135

  authored and

  altaf-ali

  committed
  410c203

• added mutation to upload a file

  Show description for 04b559d
  

  SamO135

  authored and

  altaf-ali

  committed
  04b559d

• created environment input class for mutations

  

  SamO135

  authored and

  altaf-ali

  committed
  a62ba54

• modified 'create' and 'update' query parameters

  

  SamO135

  authored and

  altaf-ali

  committed
  e0d7515

Commits on Jul 10, 2023

• allow port 5173 for the client

  SamO135

  committed
  fbc786c

Commits on Jul 13, 2023

• automatically push to the artifacts repo when creating a new environment

  SamO135

  committed
  931acde

• fix environments query not working

  SamO135

  committed
  4b68f5b

Commits on Jul 31, 2023

• update existing environment

  Show description for 3eb01d8
  SamO135

  committed
  3eb01d8

Commits on Aug 1, 2023

• optional package ids

  Show description for eadf62c
  SamO135

  committed
  eadf62c

• update error handling and responses given by graphql

  SamO135

  committed
  ad5a4b4

Commits on Aug 2, 2023

• check all fields are provided and the path is valid

  SamO135

  committed
  331d147

• delete environment mutation

  SamO135

  committed
  15a2e67

Commits on Aug 3, 2023

• prevent replacing environments when changing locations

  SamO135

  committed
  a6c40a3

Commits on Aug 7, 2023

• add file upload mutation for softpack-builder

  Show description for 58a474b
  SamO135

  committed
  58a474b

Commits on Aug 8, 2023

• format code with tox

  SamO135

  committed
  b682c9e

Commits on Aug 11, 2023

• rework update method using create_artifacts

  Show description for 634e051
  SamO135

  committed
  634e051

• rename file upload method

  Show description for 6bfc9d9
  SamO135

  committed
  6bfc9d9

• remove unused method

  SamO135

  committed
  26224f2

Commits on Aug 14, 2023

• mock testing

  SamO135

  committed
  15fc9a3

• pytest for committing to repo

  SamO135

  committed
  5aa0131

• clean up temp directory in commit test

  SamO135

  committed
  2e7fd0e

• pytest for pushing to repo

  SamO135

  committed
  c268d53

• add create file test

  SamO135

  committed
  caa43d8

• add delete environment test

  SamO135

  committed
  12297b0

Commits on Aug 15, 2023

• removed code duplication in tests

  SamO135

  committed
  d043767

• reformatted with tox

  Show description for d37febe
  SamO135

  committed
  d37febe

• format and improve code coverage

  SamO135

  committed
  52567c3

• add create environment test

  SamO135

  committed
  2f83f3d

Commits on Aug 16, 2023

• finish create environment test

  SamO135

  committed
  d822835

• 📝 docs(CODEOWNERS): add CODEOWNERS file to specify code owners for the repository

  altaf-ali

  committed
  2e1b01e

• add tests for update

  SamO135

  committed
  2663bc7

Commits on Aug 17, 2023

• add classmethod decorators back

  SamO135

  committed
  9adca64

• split create and update tests by adding a fixture

  SamO135

  committed
  d436d6a

Commits on Aug 18, 2023

• add tests for delete

  SamO135

  committed
  2e1b956

• add test for write_artifact

  SamO135

  committed
  52595d7

• add new fixture to help with tests

  Show description for af7b497
  SamO135

  committed
  af7b497

Commits on Aug 22, 2023

• Start to refactor integration tests to subdir.

  sb10

  committed
  38ffac5

Commits on Aug 23, 2023

• Refactor some replicated code and allow branch changing and checkout non-bare.

  sb10

  committed
  1ae5740

• Broken attempt at removing existing envs folder.

  sb10

  committed
  54aa3cd

• Working testable_artifacts test fixture.

  sb10

  committed
  666631c

• temp (?) hack disable ldap to avoid no-config warnings.

  sb10

  committed
  a9a8e5e

• Refactor fixture to only change settings, to allow for independent tests of clone and commit.

  sb10

  committed
  c8068d0

• Test commit and real push; change signatures to not take repo.

  sb10

  committed
  84fe41e

• Test commit and real push; change signatures to not take repo.

  sb10

  committed
  ccd0a50

• Test create_file.

  sb10

  committed
  4dda585

• Test delete_environment.

  sb10

  committed
  56bd743

• Refactor iter stuff to not be user-specific; test new iter.

  sb10

  committed
  884a217

• Move unit tests to subfolder.

  sb10

  committed
  82022fe

• Add init py.

  sb10

  committed
  2d3da1f

• Rename test_pygit to test_artifacts, and comment out all tests for now, prior to conversion to unit tests.

  sb10

  committed
  71bbdb4

Commits on Aug 24, 2023

• Delint.

  sb10

  committed
  51e9ce6

• Test environment.create().

  sb10

  committed
  9dc1816

• Test the push worked during create.

  sb10

  committed
  de1e243

• Test create.update().

  sb10

  committed
  0a502e4

• Test environment.delete().

  sb10

  committed
  31d0ed5

• Test write_artifact.

  sb10

  committed
  f681109

• Comment out tests for now until replaced with fully mocked unit tests.

  sb10

  committed
  c999436

• Update with additional testing notes.

  sb10

  committed
  fcbc2c2

• Test environment.iter().

  sb10

  committed
  562dd24

• Remove commented-out test files for now, since they had too-long lines.

  sb10

  committed
  865e590

• Reformat.

  sb10

  committed
  9e7a96a

Commits on Aug 29, 2023

• Move functions from conftest.py to utils.py.

  sb10

  committed
  21cc7a6

• Move functions from conftest.py to utils.py.

  sb10

  committed
  8a419f7

• Use fixtures for the repeated mocks.

  sb10

  committed
  6393e17

Commits on Aug 30, 2023

• Switch from env vars to markers to skip integration tests.

  sb10

  committed
  c5e516a

Commits on Aug 31, 2023

• Broken attempt at switching to bare repo: push not working.

  sb10

  committed
  5edfa94

• Fixed push to branch of bare repo; but delete deleting everything.

  sb10

  committed
  89323d6

• Fix delete_environments_folder

  sb10

  committed
  df4cacc

• Refactor tests to work with bare repo.

  sb10

  committed
  570eb2b

• Require successful push for attempted changes to be visible.

  sb10

  committed
  8f94945

• Document that this does not work on empty repo.

  sb10

  committed
  ea18ddb

• Fix test_commit_and_push() to only affect environments folder.

  sb10

  committed
  469078d

Commits on Sep 1, 2023

• Get latest repo during startup.

  sb10

  committed
  cbe4f7c

• Reformat.

  sb10

  committed
  3997c3c

• Make --repo flag work for all tests.

  sb10

  committed
  258dfb8

• Disable (unused) ldap init if no ldap config.

  sb10

  committed
  5b76224

• Add new module file parser.

  sb10

  committed
  94e08fb

• Remove unused test files.

  sb10

  committed
  9cd290e

• wip for create_from_module.

  sb10

  committed
  eb82448

Commits on Sep 4, 2023

• Add new module file parser.

  sb10

  committed
  f00b97b

• Move marker definition to ini.

  mjkw31

  committed
  a9b755d

• Make compatible with python 3.9.

  mjkw31

  committed
  f6d8ec4

• Make compatible with python 3.9, reformat and fix tests.

  mjkw31

  committed
  f369897

• Add docstrings and reformat.

  mjkw31

  committed
  45ede5a

• Remove redundant id field from Package.

  mjkw31

  committed
  26fed98

• Remove module feature for now; fix some type linting issues.

  mjkw31

  committed
  7734694

• Delint type issue.

  mjkw31

  committed
  9c0cd2c

• Note TODO that we should not hardcode URL.

  mjkw31

  committed
  a61e282

• Provide default user for git repo config and rename post fixture to httpx_post.

  mjkw31

  committed
  3bc78fc

• Change testable_environment to return a single value.

  mjkw31

  committed
  68b942a

Commits on Sep 5, 2023

• Reformat.

  mjkw31

  committed
  e2bfe67

• Remove redundant 'message' fields.

  mjkw31

  committed
  70950f1

• Remove test data for removed test.

  mjkw31

  committed
  1888722

• Rename file_was_pushed to better reflect intent.

  mjkw31

  committed
  04afd84

• Correct softpack.yaml format.

  mjkw31

  committed
  5ad16b9

• Reformat.

  mjkw31

  committed
  7f8f717

• Merge pull request #9 from wtsi-hgi/feature/mutations

  Show description for 5e84cfe
  sb10

  authored
  5e84cfe

• Fix creating new envs.

  mjkw31

  committed
  27b418e

• Merge pull request #16 from wtsi-hgi/create_fix

  Show description for acda088
  sb10

  authored
  acda088

• Add GraphQL endpoint to recieve module file to be parsed into pseudo-environment.

  mjkw31

  committed
  4ddb78f

• Allow tests to be run with additional flags (such as --repo).

  mjkw31

  committed
  baaec71

• De-linted.

  mjkw31

  committed
  0f9f7ae

• WIP: Add parameterised tests for ToSoftPack.

  mjkw31

  committed
  8319237

Commits on Sep 6, 2023

• Test edge cases for module parser.

  mjkw31

  committed
  cad405e

• Fix location of test data.

  mjkw31

  committed
  ddcaa6d

• Reformat.

  mjkw31

  committed
  e63bfed

• Generate README.md file from module path.

  mjkw31

  committed
  6e1a9c7

• Remove extra whitespace after backticks.

  mjkw31

  committed
  a524f4d

• Add docstring.

  mjkw31

  committed
  8dcb342

• Reformat.

  mjkw31

  committed
  e043039

• Correct typo.

  mjkw31

  committed
  ab51f66

• Use template to generate README.md file.

  mjkw31

  committed
  deda76e

• Add README string to environments endpoint.

  mjkw31

  committed
  f6f9a53

• Merge pull request #17 from wtsi-hgi/feature/env-from-module

  Show description for 7108d26
  sb10

  authored
  7108d26

Commits on Sep 7, 2023

• Add Environment type (softpack or module).

  mjkw31

  committed
  c942b88

• Merge pull request #18 from wtsi-hgi/feature/env-type

  Show description for 77b5d6b
  sb10

  authored
  77b5d6b

• Fix bootstrapping problem requiring at least one environment in both the users and groups directories.

  mjkw31

  committed
  7b82d85

• Merge pull request #19 from wtsi-hgi/feature/bootstrap-fix

  Show description for 5310c5b
  sb10

  authored
  5310c5b

• Add missing dependency to poetry lock file.

  mjkw31

  committed
  91acc3c

• Merge pull request #20 from wtsi-hgi/feature/fix-missing-dep

  Show description for a110326
  sb10

  authored
  a110326

Commits on Sep 8, 2023

• Split version strings from name.

  mjkw31

  committed
  68e377d

• Merge pull request #21 from wtsi-hgi/feature/split-version

  Show description for 904d2da
  sb10

  authored
  904d2da

• Allow multiple spaces after module-whatis and puts stderr statements.

  mjkw31

  committed
  5c01150

• Merge pull request #22 from wtsi-hgi/feature/fix-module-parse

  Show description for 7b32182
  sb10

  authored
  7b32182

Commits on Sep 11, 2023

• Determine environment state from artifacts.

  mjkw31

  committed
  c3aa147

• Merge pull request #23 from wtsi-hgi/feature/state

  Show description for 5b1e55a
  sb10

  authored
  5b1e55a

Commits on Sep 12, 2023

• New updateFromModule endpoint.

  mjkw31

  committed
  c9ca423

• Write multiple artifacts in a single commit.

  mjkw31

  committed
  9b85e01

• Add endpoint to create multiple artifacts in a single commit.

  mjkw31

  committed
  0f55d2c

• Remove unused Path call.

  mjkw31

  committed
  e5cb642

• Merge pull request #24 from wtsi-hgi/feature/modify-module

  Show description for d1a0939
  sb10

  authored
  d1a0939

Commits on Sep 25, 2023

• Add upload endpoint for builder to pass artifacts to be uploaded to repo.

  mjkw31

  committed
  c1fd7e6

• Use correct placeholder filename.

  mjkw31

  committed
  d649b6b

Commits on Sep 26, 2023

• Support large file uploads.

  mjkw31

  committed
  5d289de

• Add python version requirement.

  mjkw31

  committed
  246f096

• Merge pull request #25 from wtsi-hgi/feature/upload-endpoint

  Show description for 6321d7d
  sb10

  authored
  6321d7d

• Merge branch 'main' of github.com:wtsi-hgi/softpack-core into develop

  mjkw31

  committed
  679a05d

• Update spack version used in CI tests.

  mjkw31

  committed
  a429fa4

• Run CI tests on develop branch.

  mjkw31

  committed
  efd268e

• Merge pull request #28 from wtsi-hgi/main-merge

  Show description for 2ec5bf1
  sb10

  authored
  2ec5bf1