update CI

.gitlab-ci.yml

-image: centos:centos7
 pages:
+  needs: []
+  image: python:3.9
   script:
-    - yum install -y epel-release wget
-    - wget https://repo.ius.io/ius-release-el7.rpm
-    - rpm -Uvh ius-release*.rpm
-    - yum provides python3.9
-    - yum install -y python39u python39u-libs python39u-devel python39u-pip
-    - pip3.9 install -U pip
-    - pip3.9 install virtualenv
-    - virtualenv -p python3.6 venv
-    - . venv/bin/activate
-    - pip3 install sphinx
-    - yum install -y make
-    - pip3 install sphinx
-    - pip install sphinxcontrib-bibtex
-    - pip3 install sphinx_rtd_theme sphinx-argparse
-    - pip3 install -r requirements.txt
-    - pip3 install ../raiss/
-    - cd doc
-    - sphinx-apidoc -f -o ./source/_autosummary/ ../raiss/
-    - make html
-    - mv build/html/ ../public
+  - pip3 install sphinx
+  - yum install -y make
+  - pip3 install sphinx
+  - pip install sphinxcontrib-bibtex
+  - pip3 install sphinx_rtd_theme sphinx-argparse
+  - pip install -e .
+  - pip install -r doc/requirements.txt
+  - cd doc
+  - make html
+  - mv build/html/ ../public
   artifacts:
     paths:
     - public
   only:
   - master
+

doc/source/index.rst

@@ -35,6 +35,8 @@ Installation
 .. code-block:: shell
 
   pip3 install git+https://gitlab.pasteur.fr/statistical-genetics/raiss.git
+  pip3 install -r https://gitlab.pasteur.fr/statistical-genetics/raiss/-/raw/master/requirements.txt
+
 
 Alternatively, RAISS is available as a docker container: