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 Coverage Status 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 henriks from gravatar.com henriks 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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This version

84.3.0

84.2.1

84.2.0

84.1.1

84.1.0

84.0.9

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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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