chanjo

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Replace alchy with sqlservice and unfreeze SQLAlchemy

1

### This PR adds | fixes: - Fix #251 **How to prepare for test**: - Install in a local conda env -> pip install -e . (I've tested it with...

northwestwitch

Unfreeze SQLAlchemy

5

### This PR adds | fixes: - unfreeze, used with fix in https://github.com/Clinical-Genomics/chanjo-report/pull/56 **How to prepare for test**: - [ ] `ssh` to ... - [ ] Install on stage:...

dnil

Replace deprecated Alchy with SQLAlchemy

2

Alchy is discontinued and integrating chanjo in other software prevents software upgrades, see - https://github.com/Clinical-Genomics/scout/issues/4614 - https://github.com/Clinical-Genomics/scout/issues/4101

northwestwitch

Bumps [ipython](https://github.com/ipython/ipython) from 7.13.0 to 8.10.0. Release notes Sourced from ipython's releases. See https://pypi.org/project/ipython/ We do not use GitHub release anymore. Please see PyPI https://pypi.org/project/ipython/ Commits 15ea1ed release 8.10.0 560ad10...

dependabot[bot]

Bumps [certifi](https://github.com/certifi/python-certifi) from 2020.4.5.1 to 2022.12.7. Commits 9e9e840 2022.12.07 b81bdb2 2022.09.24 939a28f 2022.09.14 aca828a 2022.06.15.2 de0eae1 Only use importlib.resources's new files() / Traversable API on Python ≥3.11 ... b8eb5e9 2022.06.15.1...

dependabot[bot]

Bumps [joblib](https://github.com/joblib/joblib) from 0.14.1 to 1.2.0. Changelog Sourced from joblib's changelog. Release 1.2.0 Fix a security issue where eval(pre_dispatch) could potentially run arbitrary code. Now only basic numerics are supported....

dependabot[bot]

Bumps [mkdocs](https://github.com/mkdocs/mkdocs) from 1.1 to 1.2.3. Release notes Sourced from mkdocs's releases. 1.2.3 MkDocs 1.2.3 is a bugfix release for MkDocs 1.2. Aside: MkDocs has a new chat room on...

dependabot[bot]

Bumps [nltk](https://github.com/nltk/nltk) from 3.5 to 3.6.6. Changelog Sourced from nltk's changelog. Version 3.7 2022-02-09 Improve and update the NLTK team page on nltk.org (#2855, #2941) Drop support for Python 3.6,...

dependabot[bot]

pymysql.err.OperationalError: `(1055, "Expression #1 of SELECT list is not in GROUP BY clause and contains nonaggregated column 'chanjo4.transcript_stat.id' which is not functionally dependent on columns in GROUP BY clause; this...

northwestwitch

Bumps [py](https://github.com/pytest-dev/py) from 1.8.1 to 1.10.0. Changelog Sourced from py's changelog. 1.10.0 (2020-12-12) Fix a regular expression DoS vulnerability in the py.path.svnwc SVN blame functionality (CVE-2020-29651) Update vendored apipkg: 1.4...

dependabot[bot]