Commit 11c48e6b authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

refactor: update file tree

parents aa2f9635 0e9a0cb7
......@@ -474,5 +474,5 @@ pip-selfcheck.json
# TODO: remove line below if we want to keep eclipse metadata
.settings/
.vscode
......@@ -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.
......
This diff is collapsed.
## [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))
ARIA -- Ambiguous Restraints for Iterative Assignment
ARIA
Ambiguous Restraints for Iterative Assignment
A software for automated NOE assignment
......
......@@ -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
graft aria
graft src
graft docs
include *.md
include COPYRIGHT
......
Version: 0.0.20
\ No newline at end of file
Version: 0.1.01
\ No newline at end of file
......@@ -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
......
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())
#!/usr/bin/env bash
$PYTHON -m pip install --no-deps .
{% 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
aria.aria2 module
=================
.. automodule:: aria.aria2
:members:
:undoc-members:
:show-inheritance:
: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:
aria.check module
=================
.. automodule:: aria.check
:members:
:undoc-members:
:show-inheritance:
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment