Clinical Genomics command center

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  • Requires: Python <3.13, >=3.11
  • Provides-Extra: coveralls , mock , pre-commit , pytest , pytest-cov , pytest-freezegun , pytest-httpserver , pytest-mock , pytest-xdist , ruff
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Project description

cg

Build Status - Github GitHub issues-closed Average time to resolve an issue Percentage of issues still open CodeFactor Code style: black

cg stands for Clinical Genomics; a clinical sequencing platform under SciLifeLab

In this context, cg provides the interface between these tools to facilitate automation and other necessary cross-talk. It also exposes some APIs:

Contributing

Please check out our guide for contributing to cg

Installation

Cg written in Python 3.9+ and is available on the Python Package Index (PyPI).

pip install cg

If you would like to install the latest development version, use poetry.

git clone https://github.com/Clinical-Genomics/cg
cd cg
poetry install

For development, use poetry install --all-extras to install development dependencies.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for clingen from gravatar.com clingen Avatar for karlnyr from gravatar.com karlnyr Avatar for Vince-janv from gravatar.com Vince-janv

Unverified details

These details have not been verified by PyPI
Meta
  • Requires: Python <3.13, >=3.11
  • Provides-Extra: coveralls , mock , pre-commit , pytest , pytest-cov , pytest-freezegun , pytest-httpserver , pytest-mock , pytest-xdist , ruff
Classifiers

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87.5.0

87.4.0

87.3.0

87.2.4

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87.2.2

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87.2.1

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52.0.2

52.0.1

52.0.0

51.10.7

51.10.6

51.10.5

51.10.4

51.10.3

51.10.2

51.10.1

51.10.0

51.9.10

51.9.8

51.9.7

51.9.6

51.9.5

51.9.4

51.9.3

51.9.2

51.9.1

51.9.0

51.8.1

51.8.0

51.7.6

51.7.5

51.7.4

51.7.3

51.7.2

51.7.1

51.7.0

51.6.14

51.6.13

51.6.12

51.6.11

51.6.10

51.6.9

51.6.8

51.6.7

51.6.6

51.6.5

51.6.4

51.6.3

51.6.2

51.6.1

51.6.0

51.5.15

51.5.14

51.5.13

51.5.12

51.5.11

51.5.10

51.5.9

51.5.8

51.5.7

51.5.6

51.5.5

51.5.4

51.5.3

51.5.2

51.5.1

51.4.1

51.4.0

51.3.1

51.3.0

51.2.9

51.2.8

51.2.7

51.2.6

51.2.5

51.2.4

51.2.3

51.2.2

51.2.1

51.2.0

51.1.3

51.1.2

51.1.1

51.1.0

51.0.9

51.0.8

51.0.7

51.0.6

51.0.5

51.0.4

51.0.3

51.0.2

51.0.1

51.0.0

50.1.10

50.1.9

50.1.8

50.1.7

50.1.6

50.1.5

50.1.4

50.1.3

50.1.2

50.1.1

50.1.0

50.0.0

49.5.2

49.5.1

49.5.0

49.4.7

49.4.6

49.4.5

49.4.4

49.4.3

49.4.2

49.4.1

49.4.0

49.3.0

49.2.0

49.1.0

49.0.16

49.0.14

49.0.13

49.0.12

49.0.11

49.0.10

49.0.9

49.0.8

49.0.7

49.0.6

49.0.5

49.0.4

49.0.3

49.0.2

49.0.1

49.0.0

48.0.0

47.0.1

47.0.0

46.0.5

46.0.4

46.0.3

46.0.2

46.0.1

46.0.0

45.5.5

45.5.4

45.5.3

45.5.2

45.5.1

45.5.0

45.4.5

45.4.4

45.4.3

45.4.2

45.4.1

45.4.0

45.3.0

45.2.2

45.2.1

45.2.0

45.1.3

45.1.2

45.1.1

45.1.0

45.0.17

45.0.16

45.0.15

45.0.14

45.0.13

45.0.12

45.0.11

45.0.10

45.0.9

45.0.8

45.0.7

45.0.6

45.0.5

45.0.4

45.0.3

45.0.2

45.0.1

45.0.0

44.0.5

44.0.4

44.0.3

44.0.2

44.0.1

44.0.0

43.0.5

43.0.4

43.0.3

43.0.2

43.0.1

43.0.0

42.0.0

41.0.2

41.0.1

41.0.0

40.12.4

40.12.3

40.12.2

40.12.1

40.12.0

40.11.1

40.11.0

40.10.1

40.10.0

40.9.7

40.9.6

40.9.5

40.9.4

40.9.2

40.9.1

40.8.2

40.8.1

40.7.1

40.7.0

40.6.3

40.6.2

40.6.1

40.6.0

40.5.1

40.5.0

40.4.1

40.4.0

40.3.3

40.3.2

40.3.1

40.3.0

40.2.3

40.2.2

40.2.1

40.2.0

40.1.5

40.1.4

40.1.3

40.1.2

40.1.1

40.1.0

40.0.1

40.0.0

39.1.0

39.0.0

38.3.5

38.3.4

38.3.3

38.3.2

38.3.1

38.3.0

38.2.10

38.2.9

38.2.8

38.2.7

38.2.6

38.2.5

38.2.4

38.2.3

38.2.2

38.2.1

38.2.0

38.1.9

38.1.8

38.1.7

38.1.6

38.1.5

38.1.4

38.1.3

38.1.2

38.1.1

38.1.0

38.0.2

38.0.1

38.0.0

37.2.0

37.1.0

37.0.28

37.0.26

37.0.25

37.0.24

37.0.23

37.0.22

37.0.21

37.0.20

37.0.17

37.0.16

37.0.15

37.0.14

37.0.13

37.0.12

37.0.11

37.0.10

37.0.9

37.0.8

37.0.7

37.0.6

37.0.5

37.0.4

37.0.3

37.0.2

37.0.1

37.0.0

36.5.1

36.5.0

36.4.2

36.4.1

36.4.0

36.3.2

36.3.1

36.3.0

36.2.7

36.2.6

36.2.5

36.2.4

36.2.3

36.2.2

36.2.1

36.1.0

36.0.4

36.0.3

36.0.2

36.0.1

35.0.2

35.0.1

34.0.0

33.3.4

33.3.3

33.3.2

33.3.1

33.3.0

33.2.3

33.2.1

33.2.0

33.1.6

33.1.5

33.1.4

33.1.3

33.1.2

33.1.1

33.1.0

33.0.6

33.0.5

33.0.4

33.0.3

33.0.2

33.0.1

33.0.0

32.2.8

32.2.7

32.2.5

32.2.4

32.2.3

32.2.2

32.2.1

32.2.0

32.1.0

32.0.0

31.2.3

31.2.2

31.2.1

31.2.0

31.1.6

31.1.5

31.1.4

31.1.3

31.1.2

31.1.0

31.0.2

31.0.1

31.0.0

30.3.0

30.2.7

30.2.6

30.2.4

30.2.3

30.2.2

30.2.0

30.1.4

30.1.2

30.1.1

30.1.0

30.0.0

29.8.7

29.8.6

29.8.5

29.8.4

29.8.3

29.8.2

29.8.1

29.8.0

29.7.1

29.7.0

29.6.0

29.5.7

29.5.6

29.5.5

29.5.4

29.5.3

29.5.2

29.5.1

29.5.0

29.4.13

29.4.12

29.4.11

29.4.10

29.4.9

29.4.8

29.4.7

29.4.6

29.4.5

29.4.4

29.4.3

29.4.2

29.4.1

29.4.0

29.3.1

29.3.0

29.2.0

29.1.7

29.1.6

29.1.5

29.1.4

29.1.3

29.1.2

29.1.1

29.1.0

29.0.3

29.0.2

29.0.1

29.0.0

28.0.5

28.0.4

28.0.3

28.0.2

28.0.1

28.0.0

27.3.13

27.3.12

27.3.11

27.3.10

27.3.9

27.3.8

27.3.7

27.3.5

27.3.4

27.3.3

27.3.2

27.3.1

27.3.0

27.2.15

27.2.14

27.2.13

27.2.12

27.2.11

27.2.10

27.2.9

27.2.8

27.2.7

27.2.6

27.2.5

27.2.4

27.2.3

27.2.2

27.2.1

27.2.0

27.1.64

27.1.62

27.1.61

27.1.60

27.1.59

27.1.58

27.1.57

27.1.56

27.1.55

27.1.53

27.1.52

27.1.51

27.1.50

27.1.49

27.1.48

27.1.47

27.1.46

27.1.45

27.1.44

27.1.43

27.1.42

27.1.41

27.1.40

27.1.39

27.1.38

27.1.37

27.1.36

27.1.35

27.1.34

27.1.33

27.1.32

27.1.31

27.1.30

27.1.29

27.1.28

27.1.26

27.1.25

27.1.24

27.1.23

27.1.22

27.1.21

27.1.20

27.1.19

27.1.18

27.1.17

27.1.16

27.1.15

27.1.14

27.1.13

27.1.12

27.1.11

27.1.10

27.1.9

27.1.8

27.1.7

27.1.6

27.1.5

27.1.4

27.1.3

27.1.2

27.1.1

27.0.11

27.0.10

27.0.8

27.0.7

27.0.6

27.0.5

27.0.4

27.0.3

27.0.2

27.0.1

27.0.0

26.7.5

26.7.4

26.7.3

26.7.2

26.7.1

26.7.0

26.6.3

26.6.2

26.6.1

26.6.0

26.5.1

26.5.0

26.4.3

26.4.2

26.4.1

26.4.0

26.3.5

26.3.4

26.3.3

26.3.2

26.3.1

26.3.0

26.2.1

26.2.0

26.1.2

26.1.1

26.1.0

26.0.9

26.0.8

26.0.7

26.0.6

26.0.5

26.0.4

26.0.3

26.0.2

26.0.1

26.0.0

25.3.0

25.2.2

25.2.1

25.2.0

25.1.0

25.0.0

24.1.1

24.1.0

24.0.9

24.0.8

24.0.7

24.0.6

24.0.5

24.0.3

24.0.2

24.0.1

24.0.0

23.8.2

23.8.1

23.8.0

23.7.3

23.7.2

23.7.1

23.7.0

23.6.4

23.6.3

23.6.2

23.6.1

23.6.0

23.5.0

23.4.0

23.3.6

23.3.5

23.3.4

23.3.3

23.3.1

23.3.0

23.2.6

23.2.5

23.2.4

23.2.3

23.2.2

23.2.0

23.1.1

23.1.0

23.0.0

22.91.0

22.90.3

22.90.2

22.90.1

22.90.0

22.89.2

22.89.1

22.89.0

22.88.0

22.87.0

22.86.0

22.85.6

22.85.5

22.85.4

22.85.3

22.85.2

22.85.1

22.85.0

22.84.6

22.84.5

22.84.4

22.84.3

22.84.2

22.84.1

22.84.0

22.83.1

22.83.0

22.82.0

22.81.5

22.81.4

22.81.3

22.81.2

22.81.1

22.81.0

22.80.1

22.80.0

22.79.1

22.79.0

22.78.9

22.78.8

22.78.7

22.78.6

22.78.5

22.78.4

22.78.3

22.78.2

22.78.1

22.78.0

22.77.2

22.77.1

22.76.1

22.76.0

22.75.5

22.75.4

22.75.3

22.75.2

22.75.1

22.75.0

22.74.1

22.74.0

22.73.0

22.72.0

22.71.1

22.71.0

22.70.1

22.70.0

22.69.0

22.68.0

22.67.1

22.67.0

22.66.0

22.65.1

22.65.0

22.64.0

22.63.3

22.63.2

22.63.1

22.63.0

22.62.3

22.62.2

22.62.0

22.61.5

22.61.4

22.61.3

22.61.2

22.61.1

22.61.0

22.60.0

22.59.0

22.58.0

22.57.5

22.57.4

22.57.3

22.57.2

22.57.0

22.56.3

22.56.2

22.56.1

22.56.0

22.55.1

22.55.0

22.54.12

22.54.11

22.54.10

22.54.9

22.54.7

22.54.6

22.54.5

22.54.4

22.54.3

22.54.2

22.54.1

22.54.0

22.53.0

22.52.0

22.51.0

22.50.0

22.49.2

22.49.1

22.49.0

22.48.1

22.48.0

22.47.1

22.47.0

22.46.6

22.46.5

22.46.4

22.46.3

22.46.2

22.46.1

22.46.0

22.45.0

22.44.5

22.44.4

22.44.3

22.44.2

22.44.1

22.44.0

22.43.2

22.43.1

22.43.0

22.42.0

22.41.3

22.41.2

22.41.1

22.41.0

22.40.5

22.40.4

22.40.3

22.40.2

22.40.1

22.39.1

22.39.0

22.38.3

22.38.2

22.38.1

22.38.0

22.37.4

22.37.3

22.37.2

22.37.0

22.36.1

22.36.0

22.35.0

22.34.4

22.34.3

22.34.2

22.34.1

22.34.0

22.33.0

22.32.2

22.32.1

22.32.0

22.31.7

22.31.6

22.31.5

22.31.4

22.31.3

22.31.2

22.31.1

22.31.0

22.30.0

22.29.3

22.29.2

22.29.1

22.29.0

22.28.0

22.27.0

22.26.0

22.25.6

22.25.5

22.25.4

22.25.3

22.25.2

22.25.1

22.24.1

22.24.0

22.23.2

22.23.1

22.23.0

22.22.0

22.21.1

22.21.0

22.20.1

22.20.0

22.19.8

22.19.7

22.19.6

22.19.5

22.19.4

22.19.3

22.19.2

22.19.1

22.19.0

22.18.0

22.17.2

22.17.1

22.17.0

22.16.0

22.15.0

22.14.0

22.13.0

22.12.0

22.11.2

22.11.1

22.10.3

22.10.2

22.10.1

22.10.0

22.9.4

22.9.3

22.9.2

22.9.1

22.9.0

22.8.6

22.8.5

22.8.4

22.8.3

22.8.2

22.8.1

22.8.0

22.7.0

22.6.1

22.6.0

22.5.2

22.5.1

22.5.0

22.4.1

22.4.0

22.3.1

22.3.0

22.2.2

22.2.1

22.2.0

22.1.3

22.1.2

22.1.1

22.1.0

22.0.1

22.0.0

21.13.0

21.12.2

21.12.1

21.12.0

21.11.0

21.10.0

21.9.3

21.9.2

21.9.1

21.9.0

21.8.3

21.8.2

21.8.1

21.8.0

21.7.2

21.7.1

21.7.0

21.6.9

21.6.8

21.6.7

21.6.6

21.6.5

21.6.4

21.6.3

21.6.2

21.6.1

21.6.0

21.5.7

21.5.6

21.5.5

21.5.4

21.5.3

21.5.2

21.5.1

21.5.0

21.4.4

21.4.3

21.4.2

21.4.1

21.4.0

21.3.1

21.3.0

21.2.0

21.1.0

21.0.0

20.26.2

20.26.1

20.26.0

20.25.0

20.24.0

20.23.0

20.22.0

20.21.1

20.21.0

20.20.1

20.20.0

20.19.5

20.19.4

20.19.3

20.19.2

20.19.1

20.19.0

20.18.0

20.17.5

20.17.4

20.17.3

20.17.2

20.17.1

20.17.0

20.16.0

20.15.1

20.15.0

20.14.2

20.14.1

20.14.0

20.13.0

20.12.1

20.12.0

20.11.0

20.10.1

20.10.0

20.9.12

20.9.11

20.9.10

20.9.9

20.9.8

20.9.7

20.9.6

20.9.5

20.9.3

20.9.2

20.9.1

20.9.0

20.8.1

20.8.0

20.7.0

20.6.0

20.5.4

20.5.3

20.5.2

20.5.1

20.5.0

20.4.0

20.3.3

20.3.2

20.3.1

20.3.0

20.2.1

20.2.0

20.1.4

20.1.3

20.1.2

20.1.1

20.1.0

20.0.1

20.0.0

19.5.4

19.5.3

19.5.2

19.5.1

19.5.0

19.4.0

19.3.2

19.3.1

19.3.0

19.2.0

19.1.1

19.1.0

19.0.0

18.12.1

18.12.0

18.11.4

18.11.3

18.11.2

18.11.1

18.11.0

18.10.2

18.10.1

18.10.0

18.9.1

18.9.0

18.8.0

18.7.2

18.7.1

18.7.0

18.6.0

18.5.1

18.5.0

18.4.0

18.3.0

18.2.0

18.1.5

18.1.4

18.1.3

18.1.2

18.1.1

18.1.0

18.0.0

17.2.1

17.2.0

17.1.0

17.0.0

16.17.1

16.17.0

16.16.1

16.16.0

16.15.1

16.15.0

16.14.0

16.13.0

16.12.1

16.12.0

16.11.1

16.11.0

16.10.4

16.10.3

16.10.2

16.10.1

16.10.0

16.9.0

16.8.1

16.8.0

16.7.1

16.7.0

16.6.0

16.5.0

16.4.3

16.4.2

16.4.1

16.4.0

16.3.4

16.3.3

16.3.2

16.3.1

16.3.0

16.2.0

16.1.1

16.1.0

16.0.6

16.0.5

16.0.4

16.0.3

16.0.2

16.0.1

16.0.0

15.0.4

15.0.3

15.0.2

15.0.1

15.0.0

14.0.1

14.0.0

13.18.0

13.17.2

13.17.1

13.17.0

13.16.2

13.16.1

13.16.0

13.15.0

13.14.3

13.14.2

13.14.1

13.14.0

13.13.0

13.12.1

13.12.0

13.11.0

13.10.1

13.10.0

13.9.0

13.8.0

13.7.0

13.6.0

13.5.0

13.4.1

13.4.0

13.3.1

13.3.0

13.2.0

13.1.0

13.0.0

12.7.1

12.7.0

12.6.0

12.5.0

12.4.0

12.3.6

12.3.5

12.3.4

12.3.3

12.3.2

12.3.1

12.3.0

12.2.0

12.1.7

12.1.6

12.1.5

12.1.4

12.1.3

1.0.0

1.0.0b2 pre-release

0.9.1

0.9.0

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