Merge branch '30-pip-installation' into 'master'

Resolve "pip installation"

Closes #30

See merge request bis-aria/ariaec!9

.gitlab-ci.yml

@@ -18,8 +18,6 @@ build:
     - docker login -u gitlab-ci-token -p "$CI_BUILD_TOKEN" registry-gitlab.pasteur.fr
     - docker build --pull -t "$CI_REGISTRY_IMAGE:$CI_BUILD_REF_NAME" .
     - docker push "$CI_REGISTRY_IMAGE:$CI_BUILD_REF_NAME"
-  only:
-    - master
 
 pytest:
   image: registry-gitlab.pasteur.fr/bis-aria/ariaec:$CI_BUILD_REF_NAME

Dockerfile

@@ -2,18 +2,18 @@ FROM centos:centos7
 MAINTAINER Fabrice Allain <fabrice.allain@pasteur.fr>
 
 RUN yum install -y epel-release
-RUN yum install -y python2-pip python-devel gcc make git
+RUN yum install -y python2-pip python-devel gcc gcc-c++ make git
 RUN curl --silent --location https://rpm.nodesource.com/setup_8.x | bash -; yum -y install nodejs
 
 RUN npm install -g --save-dev @commitlint/{cli,config-conventional}; npm install -g conventional-changelog-cli
 RUN echo "module.exports = {extends: ['@commitlint/config-conventional']};" > commitlint.config.js
 
-RUN pip install --upgrade pip ; pip install --upgrade setuptools; pip install sphinx; pip install numpy; pip install matplotlib; pip install coverage; pip install pytest; pip install pytest-cov
+RUN pip install --upgrade pip ; pip install --upgrade setuptools; pip install coverage; pip install pytest; pip install pytest-cov
 
 RUN wget http://www2.ccpn.ac.uk/download/ccpnmr/analysis2.4.2.tar.gz; tar xvzf analysis2.4.2.tar.gz; export CCPNMR_TOP_DIR=$(pwd)/ccpnmr; export PYTHONPATH=${PYTHONPATH}:$CCPNMR_TOP_DIR/ccpnmr2.4/python
 
-RUN mkdir build-aria
-ADD aria /build-aria/aria
+RUN mkdir build-aria && mkdir build-aria/src
+ADD src/aria /build-aria/src/aria
 ADD *.py PKG-INFO /build-aria/
 RUN cd build-aria && pip install .; npm install --save-dev husky
 RUN npx yarn add husky --dev

MANIFEST.in

-graft aria
+graft src
 graft docs
 include *.md
 include COPYRIGHT

conda.recipe/build.sh

+#!/usr/bin/env bash
+$PYTHON -m pip install --no-deps .

conda.recipe/meta.yaml

+{% set data = load_setup_py_data() %}
+
+package:
+  name: ariaec
+  version: {{ data['version'] }}
+
+source:
+  path: ..
+
+build:
+  # If the installation is complex, or different between Unix and Windows, use
+  # separate bld.bat and build.sh files instead of this key.  Add the line
+  # "skip: True  # [py<35]" (for example) to limit to Python 3.5 and newer, or
+  # "skip: True  # [not win]" to limit to Windows.
+#  script: python setup.py install --single-version-externally-managed --record=record.txt
+#  number: {{ environ.get('CI_PIPELINE_ID', 0) }}
+
+requirements:
+  build:
+    - python
+    - setuptools
+
+  run:
+    - python
+    - # dependencies are defined in setup.py
+    {% for dep in data['install_requires'] %}
+    - {{ dep.lower() }}
+    {% endfor %}
+
+test:
+  requires:
+    - bandit
+    - pylint
+    - pytest
+    - pytest-cov
+
+  imports:
+    - ariaec
+
+about:
+  summary: "de Novo Ambiguous Restraints for Iterative Assignment"
+  home: https://gitlab.pasteur.fr/bis-aria/ariaec
+#  license: Proprietary
+  extra:
+    sphinx:
+      language: en
+      intersphinx:
+        # project: Parent URL of the "objects.inv" file

setup.py

@@ -206,10 +206,14 @@ def setup_package():
         setup_requires=[
             # Setuptools 18.0 properly handles Cython extensions.
             'setuptools>=18.0',
-            'cython',
+            'cython>=0.16',
+            'numpy>=1.10.4',
+            'biopython==1.73',
+            'scipy<1.3.0',
             'matplotlib<3.0',
-            'numpy',
-            'pytest-runner'
+            'pytest-runner',
+            'networkx==2.2',
+            'MDAnalysis'
         ],
         tests_requires=['pytest', 'pytest-cov'],
         # Project uses reStructuredText, so ensure that the docutils get
@@ -228,8 +232,6 @@ def setup_package():
             # 'sphinxcontrib-napoleon',
             'configparser',
             'mako',
-            'biopython>=1.69',
-            'scipy>= 0.9',
             'pandas',
             'seaborn',
             'sklearn',
@@ -257,8 +259,8 @@ def setup_package():
         },
         # bin folder is normally for non python code that could be executed
         # directly on terminal (bash scripts, ...)
-        scripts=['aria/aria2.py',
-                 'aria/check.py'],
+        scripts=['src/aria/aria2.py',
+                 'src/aria/check.py'],
         # Force setuptools to unzip in order to access data files with pkgutil
         # since pkg_resources don't like relative paths in zipped egg dir :/
         # TODO: solution to enable zip_safe
@@ -271,7 +273,9 @@ def setup_package():
         # to respect pep recommandations. Non data files can be includes outside
         # the package with data_files key (non data files are not accessible by
         # the package after the installation)
-        # package_dir={
+        package_dir={
+            '': 'src'
+        },
         #     '': 'src/py',
         #     'aria': 'src/py/aria',
         #     'aria.cns': 'cns',
@@ -284,7 +288,9 @@ def setup_package():
         #     'aria.src.xml': 'src/xml',
         #     'aria.src.csh': 'src/csh'},
 
-        packages=find_packages(exclude=("examples*",)),
+        packages=find_packages("src", exclude=("docs*",)),
+        # Line below works for Python 3 only
+        # packages=find_namespace_packages(where='src'),
 
         # Install any data files found in the package
         include_package_data=True,