refactor: update file tree

.gitignore

@@ -474,5 +474,5 @@ pip-selfcheck.json
 
 # TODO: remove line below if we want to keep eclipse metadata
 .settings/
-
+.vscode
 

.gitlab-ci.yml

@@ -15,14 +15,18 @@ stages:
 build:
   stage: build
   script:
-    - 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:$CI_BUILD_REF_NAME"
+    - docker login -u gitlab-ci-token -p "$CI_JOB_TOKEN" registry-gitlab.pasteur.fr
+    - docker build --pull -t "$CI_REGISTRY_IMAGE:latest" .
+    - docker push "$CI_REGISTRY_IMAGE:latest"
   only:
-    - master
+    changes:
+      - .gitlab-ci.yml
+      - Dockerfile
+      - package.json
+      - setup.py
 
 pytest:
-  image: registry-gitlab.pasteur.fr/bis-aria/ariaec:$CI_BUILD_REF_NAME
+  image: $CI_REGISTRY_IMAGE:latest
   stage: test
   script:
     - cd ${CI_PROJECT_DIR}
@@ -31,16 +35,22 @@ pytest:
 
 coverage:
   stage: coverage
-  image: registry-gitlab.pasteur.fr/bis-aria/ariaec:$CI_BUILD_REF_NAME
+  image: $CI_REGISTRY_IMAGE:latest
   script:
     - pytest --cov=aria --cov-report html --cov-report term
   coverage: '/TOTAL.+ ([0-9]{1,3}%)/'
   artifacts:
     paths:
       - htmlcov/
-
+  only:
+    refs:
+      - production
+      - master
+    changes:
+      - src/**/*
+    
 pages:
-  image: registry-gitlab.pasteur.fr/bis-aria/ariaec:$CI_BUILD_REF_NAME
+  image: $CI_REGISTRY_IMAGE:latest
   stage: deploy
   dependencies:
     - coverage
@@ -54,14 +64,31 @@ pages:
     paths:
       - public
   only:
-    - master
+    refs:
+      - master
+      - production
+    changes:
+      - docs/**/*
 
 cleanup_pypirc:
   stage: cleanup
   when: always   # this is important; run even if preceding stages failed.
   script:
     - rm -vf ~/.pypirc  # we don't want to leave these around, but GitLab may clean up anyway.
-    
+
+deliver:
+  image:
+    name: registry.gitlab.com/hyper-expanse/open-source/semantic-delivery-gitlab:9.0.0
+    entrypoint: [""]
+  script:
+    - semantic-delivery-gitlab --token $SEMANTIC_TOKEN
+  stage: deploy
+  environment:
+    name: production
+  only:
+    - production
+
+
 # deploy_pypi:
 #     stage: deploy
 #     script:   # Configure the PyPI credentials, then push the package, and cleanup the creds.

CHANGELOG.md

+## [0.0.21](https://gitlab.pasteur.fr/bis-aria/Ariaec/compare/0.1.0...0.0.21) (2019-07-08)
+
+
+### Bug Fixes
+
+* add debug log message in ssclash ([8e50b10](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8e50b10))
+* add debug log message in ssclash ([beb4935](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/beb4935))
+* avoid key errors if all parameters don't exist with pdbqual command ([ea0e556](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ea0e556))
+* change api key for semantic delivery ([8eba464](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8eba464))
+* change dependencies in setup.py ([eb5c0be](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/eb5c0be))
+* change depreacted CI var in gitlab ci conf file ([74463c0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/74463c0))
+* change depreacted CI var in gitlab ci conf file ([4464019](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4464019))
+* escape percent character within csh script for format function ([a785ce9](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a785ce9))
+* force python 2.7 dependency ([99041c7](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/99041c7))
+* force python 2.7 dependency ([5f3380d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5f3380d))
+* future dependency in dockerfile ([0d1d39e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0d1d39e))
+* implement setting.get method used within pdbqual tool ([a8d66dc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a8d66dc))
+* implement setting.get method used within pdbqual tool ([1832c26](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1832c26))
+* remove logger during serialization for distance restraint class ([0465e1b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0465e1b))
+* remove sge_job_id var in csh script refine for sbatch options ([a036e7f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a036e7f))
+* removed unicode strings during convert part ([39d1d47](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/39d1d47))
+* revision of output slurm file for cns refine.csh ([8d14ebd](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8d14ebd))
+* solve conflict issue between pdbqual and setup config parameters ([48a05e2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/48a05e2))
+* solve import issue with pdbqual command ([737dd53](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/737dd53))
+* solve issue [#24](https://gitlab.pasteur.fr/bis-aria/Ariaec/issues/24) ([aeda4d1](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/aeda4d1))
+* solve issue with missing alignment for evcoupling contacts ([c6f3afc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c6f3afc))
+* solve issue with warnings in the logger ([990419e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/990419e))
+* solve numpy dependency issue with hdbscan ([bf3c81c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bf3c81c))
+* solve several format issues in the new logging system ([eff5776](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/eff5776))
+* sphinx crash with 1.8 due to python 3 dependencies ([fd0efa1](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/fd0efa1))
+* syntax error for clashlist flag in aria project templates ([9b270f0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9b270f0))
+* Update ariabase.py getstate ([6c209af](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6c209af))
+* update doc confs with the new project tree ([46dff44](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/46dff44))
+* update dockerfile ([541d72c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/541d72c))
+* update dockerfile ([40b59e9](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/40b59e9))
+* update dockerfile ([00d6865](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/00d6865))
+* wget dependency in dockerfile ([bdf572c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/bdf572c))
+* wrong installation order in dockerfile for husky npm module ([934a449](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/934a449))
+* wrong installation order in dockerfile for husky npm module ([c83c314](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c83c314))
+* **aria.core.TypeChecking:** overwrite previous python3 patch ([dbca55a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/dbca55a))
+* **aria.core.TypeChecking:** solve byte string type checker issue when running the package with python3 ([07fb1c6](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/07fb1c6))
+
+
+### Features
+
+* add options to activate or deactivate pdq quality tools (pdbqual command) ([4a54d05](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4a54d05))
+* add structure_analysis_enabled option within conbox commands ([e88a654](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e88a654))
+* add v2.3.7 aria project template ([1b9fa48](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1b9fa48))
+* Automatic changelog ([8fda476](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8fda476))
+* Automatic changelog ([23e095b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/23e095b))
+* molecule settings hack in order to support multiple chains ([164f187](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/164f187))
+* new logging system for aria core ([223c58d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/223c58d))
+* new logging system for aria core ([1fd579c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/1fd579c))
+* safe xml tag checker for python3 ([d8b091e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d8b091e))
+* semantic delivery gitlab ([b11664f](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b11664f))
+
+
+

COPYRIGHT → COPYRIGHT.md

-          ARIA -- Ambiguous Restraints for Iterative Assignment
+                                ARIA 
+          
+            Ambiguous Restraints for Iterative Assignment
 
                  A software for automated NOE assignment
 

Dockerfile

@@ -2,18 +2,20 @@ 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 wget which
 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 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 ls build-aria/src/aria
+RUN which pip; which python
+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

PKG-INFO

-Version: 0.0.20
\ No newline at end of file
+Version: 0.1.01
\ No newline at end of file

README.md

@@ -21,18 +21,21 @@ list of PDB files.
 Be sure to check if the following packages are correctly installed with
 your python installation or virtual environment.
 
-- **pip** (>= 9.0)
-- **setuptools** (>= 18.0)
+- **pip** (>= 18.0)
+- **git** (>= 2.0)
 - **cns-solve** (1.21)
+- **ccpnmr analysis** (optional)
+- **ccpn data model** (optional)
 
 Then the easiest solution is to call the **pip** command below :
 
-   `pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec`
+   `pip install --user git+http://gitlab.pasteur.fr/bis-aria/ariaec.git`
 
 For more information about installation and usage, please refer to the
 [ARIAEC documentation](http://bis-aria.pages.pasteur.fr/ariaec)
 
-**ARIA contains patches for CNS-solve which needs to be compiled after the installation. Please follow [post installation instructions](http://bis-aria.pages.pasteur.fr/ariaec/installation.html#post-installation-instructions).**
+**ARIA contains patches for CNS-solve which needs to be compiled after the
+installation. Please follow [post installation instructions](http://bis-aria.pages.pasteur.fr/ariaec/installation.html#post-installation-instructions).**
 
     
 ## Contributing

aria/core/test/test_AriaXML.py

-import os
-import pytest
-from aria.core.Settings import Path
-from aria.core.AriaXML import AriaXMLPickler
-from aria.core.ariabase import PROJECT_TEMPLATE, AriaBaseClass
-
-
-@pytest.fixture
-def pickler():
-    return AriaXMLPickler()
-
-
-@pytest.fixture
-def projectemplate():
-    return os.path.join(AriaBaseClass.data_path, PROJECT_TEMPLATE)
-
-
-@pytest.fixture
-def project(pickler, projectemplate):
-    Path.global_mandatory = 0
-    return pickler.load_relaxed(projectemplate)
-
-
-def test_pickler_create_document(project, pickler):
-    pickler.create_document(project)
-
-
-def test_pickler_dumps(project, pickler):
-    pickler.dumps(project)
-
-
-if __name__ == '__main__':
-    print("Test load aria xml template")
-    test_pickler_create_document(project(pickler(), projectemplate()), pickler())
-    test_pickler_dumps(project(pickler(), projectemplate()), pickler())
-

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

docs/api/aria.aria2.rst

+aria.aria2 module
+=================
+
+.. automodule:: aria.aria2
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/aria.ariacns.rst

-
-:autogenerated:
-
 aria.ariacns module
 ===================
 
-.. currentmodule:: aria.ariacns
-
 .. automodule:: aria.ariacns
-   :members: CNSPatchCommand, main
-   :undoc-members:
-   :show-inheritance:
-   :member-order: bysource
-
-Summary
--------
-
-Classes:
-
-.. autosummary::
-   :nosignatures:
-
-   CNSPatchCommand
-
-Functions:
-
-.. autosummary::
-   :nosignatures:
-
-   main
-
-
-
-
-
-Reference
----------
\ No newline at end of file
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/aria.check.rst

+aria.check module
+=================
+
+.. automodule:: aria.check
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/aria.conbox.analysis.rst

@@ -7,7 +7,7 @@ aria.conbox.analysis module
 .. currentmodule:: aria.conbox.analysis
 
 .. automodule:: aria.conbox.analysis
-   :members: EnsembleAnalysis, colscatter
+   :members: DATA_SEQUENCE, EnsembleAnalysis, colscatter
    :undoc-members:
    :show-inheritance:
    :member-order: bysource
@@ -29,6 +29,13 @@ Functions:
 
    colscatter
 
+Data:
+
+.. autosummary::
+   :nosignatures:
+
+   DATA_SEQUENCE
+
 
 
 

docs/api/aria.conbox.commands.rst

@@ -7,7 +7,7 @@ aria.conbox.commands module
 .. currentmodule:: aria.conbox.commands
 
 .. automodule:: aria.conbox.commands
-   :members: AriaEcCommands, CLI, ReadableDir, ReadableFile, check_file, main, seqrange_type
+   :members: AriaEcCommands, CLI, CONTACT_FILE_PARSERS, ReadableDir, ReadableFile, check_file, conboxdoc, main, seqrange_type
    :undoc-members:
    :show-inheritance:
    :member-order: bysource
@@ -34,6 +34,14 @@ Functions:
    main
    seqrange_type
 
+Data:
+
+.. autosummary::
+   :nosignatures:
+
+   CONTACT_FILE_PARSERS
+   conboxdoc
+
 
 
 

docs/api/aria.conbox.common.rst

@@ -7,7 +7,7 @@ aria.conbox.common module
 .. currentmodule:: aria.conbox.common
 
 .. automodule:: aria.conbox.common
-   :members: Capturing, CommandProtocol, CustomLogging, NotDisordered, RedirectStdStreams, TqdmToLogger, addtup, cart_dist, format_dict, format_str, get_filename, parmap, ppdict, reg_load, sort_2dict, tickmin, tickrot, titleprint, worker
+   :members: AbcLogFilter, Capturing, CommandProtocol, CustomLogging, NotDisordered, RedirectStdStreams, TqdmToLogger, addtup, cart_dist, format_dict, format_str, get_filename, parmap, ppdict, reg_load, sort_2dict, tickmin, tickrot, titleprint, worker
    :undoc-members:
    :show-inheritance:
    :member-order: bysource
@@ -20,6 +20,7 @@ Classes:
 .. autosummary::
    :nosignatures:
 
+   AbcLogFilter
    Capturing
    CommandProtocol
    CustomLogging

docs/api/aria.conbox.converter.rst

@@ -7,7 +7,7 @@ aria.conbox.converter module
 .. currentmodule:: aria.conbox.converter
 
 .. automodule:: aria.conbox.converter
-   :members: AriaEcBbConverter, AriaEcConfigConverter, AriaEcXMLConverter, AriaXMLConverter
+   :members: AriaEcBbConverter, AriaEcConfigConverter, AriaEcXMLConverter, AriaXMLConverter, DATA_ANNEALING_RDC, DATA_RDCS, DATA_SEQUENCE, DATA_TYPES
    :undoc-members:
    :show-inheritance:
    :member-order: bysource
@@ -25,6 +25,16 @@ Classes:
    AriaEcXMLConverter
    AriaXMLConverter
 
+Data:
+
+.. autosummary::
+   :nosignatures:
+
+   DATA_ANNEALING_RDC
+   DATA_RDCS
+   DATA_SEQUENCE
+   DATA_TYPES
+
 
 
 

docs/api/aria.conbox.pdbqual.rst

@@ -7,7 +7,7 @@ aria.conbox.pdbqual module
 .. currentmodule:: aria.conbox.pdbqual
 
 .. automodule:: aria.conbox.pdbqual
-   :members: AriaEcPdbqual
+   :members: AriaEcPdbqual, FILENAME_REPORT
    :undoc-members:
    :show-inheritance:
    :member-order: bysource
@@ -22,6 +22,13 @@ Classes:
 
    AriaEcPdbqual
 
+Data:
+
+.. autosummary::
+   :nosignatures:
+
+   FILENAME_REPORT
+