Move extras_require to setup.py

.gitlab-ci.yml

@@ -38,10 +38,6 @@ containers:
 .test-python: &test-python
   stage: initial
   image: python
-  before_script:
-    # this is required because pytables doesn't use a wheel on py37
-    - apt-get -yqq update
-    - apt-get -yqq install libhdf5-dev
   script:
     - python -m pip install .
     - python -m pip list installed
@@ -109,6 +105,15 @@ precommits-py3.9:
 #    CACHE_DIR: ".pip310"
 #    PYVERSION: "python310"
 
+install:
+  stage: initial
+  parallel:
+    matrix:
+      - EXTRA: [gw, mcmc, all]
+  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
+  script:
+    - pip install .[$EXTRA]
+
 # ------------------- Test stage -------------------------------------------
 
 .unit-tests: &unit-test

MANIFEST.in

 include README.rst
 include LICENSE.md
 include requirements.txt
+include gw_requirements.txt
+include mcmc_requirements.txt
+include optional_requirements.txt
+include sampler_requirements.txt
 recursive-include test *.py *.prior

gw_requirements.txt

+astropy>=5
+lalsuite
+gwpy
+tables
+pyfftw

mcmc_requirements.txt

+scikit-learn
+nflows

optional_requirements.txt

-astropy
 celerite
-lalsuite
 george
-gwpy
-theano
 plotly
-tables
-pyfftw
-scikit-learn
-nflows

requirements.txt

@@ -8,6 +8,4 @@ pandas
 dill
 tqdm
 h5py
-tables
-astropy
-attrs
\ No newline at end of file
+attrs

setup.cfg

@@ -16,11 +16,5 @@ addopts =
 name = bilby
 license_file = LICENSE.md
 
-[options.extras_require]
-gw =
-	astropy
-	gwpy
-	lalsuite
-
 [isort]
 known_third_party = astropy,attr,bilby,deepdish,gwin,gwinc,gwpy,lal,lalsimulation,matplotlib,mock,nflows,numpy,packaging,pandas,past,pycbc,pymc3,pytest,scipy,setuptools,skimage,torch

setup.py

@@ -56,8 +56,12 @@ def get_long_description():
     return long_description
 
 
-def get_requirements():
-    with open("requirements.txt", "r") as ff:
+def get_requirements(kind=None):
+    if kind is None:
+        fname = "requirements.txt"
+    else:
+        fname = f"{kind}_requirements.txt"
+    with open(fname, "r") as ff:
         requirements = ff.readlines()
     return requirements
 
@@ -107,6 +111,16 @@ setup(
     },
     python_requires=">=3.8",
     install_requires=get_requirements(),
+    extras_require={
+        "gw": get_requirements("gw"),
+        "mcmc": get_requirements("mcmc"),
+        "all": (
+            get_requirements("sampler")
+            + get_requirements("gw")
+            + get_requirements("mcmc")
+            + get_requirements("optional")
+        ),
+    },
     entry_points={
         "console_scripts": [
             "bilby_plot=cli_bilby.plot_multiple_posteriors:main",