Commit be5afca4 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

Merge branch '3-uniformization-of-docs-between-aria-and-conbox'

parents b033604a 5f3380d7
......@@ -51,8 +51,6 @@ pages:
artifacts:
paths:
- public
only:
- master
cleanup_pypirc:
stage: cleanup
......
......@@ -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 gcc-c++ 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 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 && 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
aria.aria2 module
=================
.. automodule:: aria.aria2
:members:
:undoc-members:
:show-inheritance:
aria.ariacns module
===================
.. automodule:: aria.ariacns
: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, 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
......@@ -21,6 +21,8 @@ Classes:
:nosignatures:
AriaEcCommands
CLI
ReadableDir
ReadableFile
Functions:
......@@ -32,6 +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
......
......@@ -7,7 +7,7 @@ aria.core.Analyser module
.. currentmodule:: aria.core.Analyser
.. automodule:: aria.core.Analyser
:members: Analyser, AnalyserXMLPickler, AnalysisParameters
:members: ALWAYS, ARIA_ENV, ARRAY, Analyser, AnalyserXMLPickler, AnalysisParameters, BOOL, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
......@@ -24,6 +24,38 @@ Classes:
AnalyserXMLPickler
AnalysisParameters
Data:
.. autosummary::
:nosignatures:
ALWAYS
ARIA_ENV
ARRAY
BOOL
CCPN_EXTENSION
DICT
FLOAT
FLOAT64
GZIP
INT
LIST
MODULE_NAME
NO
NONE
ORDEREDICT
PATH_MODULES
PRINT_LOCK
PROJECT_TEMPLATE
STRING
TUPLE
TYPES
UNICODE
VL_LOW
VL_SETTINGS
VL_STANDARD
YES
......
......@@ -7,7 +7,7 @@ aria.core.AriaPeak module
.. currentmodule:: aria.core.AriaPeak
.. automodule:: aria.core.AriaPeak
:members: AbstractPeak, AriaPeak, AriaPeakAnalysis, AriaPeakAnalysisXMLPickler, AriaPeakListTextPickler, AriaPeakListTextPicklerSettings, AriaPeakTextPickler, AriaPeakXMLPickler, ContributionTextPickler, DistanceRestraint, DistanceRestraintXMLPickler, TextPickler
:members: ABBREVIATIONS_CONTRIBUTIONS, ALWAYS, ARIA_ENV, ARRAY, ASSIGNMENT_TYPE_DICT, AbstractPeak, AriaPeak, AriaPeakAnalysis, AriaPeakAnalysisXMLPickler, AriaPeakListTextPickler, AriaPeakListTextPicklerSettings, AriaPeakTextPickler, AriaPeakXMLPickler, BOOL, CCPN_EXTENSION, CONTRIBUTIONS_HEADER, CONTRIBUTION_SINGLE, CONTRIBUTION_SPINPAIR, ContributionTextPickler, DICT, DistanceRestraint, DistanceRestraintXMLPickler, FLOAT, FLOAT64, GZIP, HEADER_ABBREVIATIONS, HEADER_AMBIG, HEADER_ASSIGNMENT_TYPE, HEADER_DICT, HEADER_PROJECT, HEADER_RESTRAINT_ACTIVE, HEADER_RESTRAINT_BOUNDS, HEADER_RESTRAINT_DEFINITION, HEADER_SEQUENCE_SEPARATION, HEADER_UNAMBIG, HEADER_VIOLATIONS, INT, LIST, MODULE_NAME, NA, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, TextPickler, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
......@@ -33,6 +33,55 @@ Classes:
DistanceRestraintXMLPickler
TextPickler
Data:
.. autosummary::
:nosignatures:
ABBREVIATIONS_CONTRIBUTIONS
ALWAYS
ARIA_ENV
ARRAY
ASSIGNMENT_TYPE_DICT
BOOL
CCPN_EXTENSION
CONTRIBUTIONS_HEADER
CONTRIBUTION_SINGLE
CONTRIBUTION_SPINPAIR
DICT
FLOAT
FLOAT64
GZIP
HEADER_ABBREVIATIONS
HEADER_AMBIG
HEADER_ASSIGNMENT_TYPE
HEADER_DICT
HEADER_PROJECT
HEADER_RESTRAINT_ACTIVE
HEADER_RESTRAINT_BOUNDS
HEADER_RESTRAINT_DEFINITION
HEADER_SEQUENCE_SEPARATION
HEADER_UNAMBIG
HEADER_VIOLATIONS
INT
LIST
MODULE_NAME
NA
NO
NONE
ORDEREDICT
PATH_MODULES
PRINT_LOCK
PROJECT_TEMPLATE
STRING
TUPLE
TYPES
UNICODE
VL_LOW
VL_SETTINGS
VL_STANDARD
YES
......
......@@ -7,7 +7,7 @@ aria.core.AriaXML module
.. currentmodule:: aria.core.AriaXML
.. automodule:: aria.core.AriaXML
:members: AriaXMLContentHandler, AriaXMLPickler, DOCManager
:members: ALWAYS, ARIA_ENV, ARRAY, AriaXMLContentHandler, AriaXMLPickler, BOOL, CCPN_EXTENSION, DICT, DOCManager, DOCTYPE_DIST_RESTRAINTS, DOCTYPE_NOE_RESTRAINTS, DTD_CHEMICAL_SHIFT_LIST, DTD_DIST_RESTRAINT, DTD_MOLECULE, DTD_NOESY_SPECTRUM, DTD_NOE_RESTRAINT, DTD_PROJECT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
......@@ -24,6 +24,46 @@ Classes:
AriaXMLPickler
DOCManager
Data:
.. autosummary::
:nosignatures:
ALWAYS
ARIA_ENV
ARRAY
BOOL
CCPN_EXTENSION
DICT
DOCTYPE_DIST_RESTRAINTS
DOCTYPE_NOE_RESTRAINTS
DTD_CHEMICAL_SHIFT_LIST
DTD_DIST_RESTRAINT
DTD_MOLECULE
DTD_NOESY_SPECTRUM
DTD_NOE_RESTRAINT
DTD_PROJECT
FLOAT
FLOAT64
GZIP
INT
LIST
MODULE_NAME
NO
NONE
ORDEREDICT
PATH_MODULES
PRINT_LOCK
PROJECT_TEMPLATE
STRING
TUPLE
TYPES
UNICODE
VL_LOW
VL_SETTINGS
VL_STANDARD
YES
......
......@@ -7,7 +7,7 @@ aria.core.Assignment module
.. currentmodule:: aria.core.Assignment
.. automodule:: aria.core.Assignment
:members: Assignment, AssignmentXMLPickler
:members: ASSIGNMENT_TYPES, ASSIGNMENT_TYPE_AUTOMATIC, ASSIGNMENT_TYPE_MANUAL, Assignment, AssignmentXMLPickler
:undoc-members:
:show-inheritance:
:member-order: bysource
......@@ -23,6 +23,15 @@ Classes:
Assignment
AssignmentXMLPickler
Data:
.. autosummary::
:nosignatures:
ASSIGNMENT_TYPES
ASSIGNMENT_TYPE_AUTOMATIC
ASSIGNMENT_TYPE_MANUAL
......
......@@ -7,7 +7,7 @@ aria.core.AssignmentFilter module
.. currentmodule:: aria.core.AssignmentFilter
.. automodule:: aria.core.AssignmentFilter
:members: AssignmentFilter
:members: ALWAYS, ARIA_ENV, ARRAY, AssignmentFilter, BOOL, CCPN_EXTENSION, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
......@@ -22,6 +22,38 @@ Classes:
AssignmentFilter
Data:
.. autosummary::
:nosignatures:
ALWAYS
ARIA_ENV
ARRAY
BOOL
CCPN_EXTENSION
DICT
FLOAT
FLOAT64
GZIP
INT
LIST
MODULE_NAME
NO
NONE
ORDEREDICT
PATH_MODULES
PRINT_LOCK
PROJECT_TEMPLATE
STRING
TUPLE
TYPES
UNICODE
VL_LOW
VL_SETTINGS
VL_STANDARD
YES
......
......@@ -7,7 +7,7 @@ aria.core.Atom module
.. currentmodule:: aria.core.Atom
.. automodule:: aria.core.Atom
:members: Atom, AtomSettings, AtomXMLPickler
:members: ARRAY, Atom, AtomSettings, AtomXMLPickler, BOOL, DICT, FLOAT, FLOAT64, INT, LIST, NONE, NOT_INIT, ORDEREDICT, STRING, TUPLE, TYPES, UNICODE
:undoc-members:
:show-inheritance:
:member-order: bysource
......@@ -24,6 +24,26 @@ Classes:
AtomSettings
AtomXMLPickler
Data:
.. autosummary::
:nosignatures:
ARRAY
BOOL
DICT
FLOAT
FLOAT64
INT
LIST
NONE
NOT_INIT
ORDEREDICT
STRING
TUPLE
TYPES
UNICODE
......
......@@ -7,7 +7,7 @@ aria.core.Chain module
.. currentmodule:: aria.core.Chain
.. automodule:: aria.core.Chain
:members: AtomNomenclatureEntity, Chain, ChainSettings, ChainXMLPickler
:members: ALWAYS, ARIA_ENV, ARRAY, AtomNomenclatureEntity, BOOL, CCPN_EXTENSION, Chain, ChainSettings, ChainXMLPickler, DICT, FLOAT, FLOAT64, GZIP, INT, LIST, MODULE_NAME, NO, NONE, ORDEREDICT, PATH_MODULES, PRINT_LOCK, PROJECT_TEMPLATE, STRING, TUPLE, TYPES, TYPE_DNA, TYPE_NONPOLYMER, TYPE_PROTEIN, TYPE_RNA, UNICODE, VL_LOW, VL_SETTINGS, VL_STANDARD, YES
:undoc-members:
:show-inheritance:
:member-order: bysource
......@@ -25,6 +25,42 @@ Classes:
ChainSettings
ChainXMLPickler
Data:
.. autosummary::
:nosignatures:
ALWAYS
ARIA_ENV
ARRAY
BOOL
CCPN_EXTENSION
DICT
FLOAT
FLOAT64
GZIP
INT
LIST
MODULE_NAME
NO
NONE
ORDEREDICT
PATH_MODULES
PRINT_LOCK
PROJECT_TEMPLATE
STRING
TUPLE
TYPES
TYPE_DNA
TYPE_NONPOLYMER
TYPE_PROTEIN
TYPE_RNA
UNICODE
VL_LOW
VL_SETTINGS
VL_STANDARD
YES
......
......@@ -7,7 +7,7 @@ aria.core.ChemicalShiftFilter module
.. currentmodule:: aria.core.ChemicalShiftFilter
.. automodule:: aria.core.ChemicalShiftFilter
:members: ChemicalShiftFilter, ChemicalShiftFilterSettings
:members: ChemicalShiftFilter, ChemicalShiftFilterSettings, INVALID_SHIFT_VALUE, NEGATIVE_SHIFT_ERROR
:undoc-members:
:show-inheritance:
:member-order: bysource
......@@ -23,6 +23,14 @@ Classes:
ChemicalShiftFilter
ChemicalShiftFilterSettings
Data:
.. autosummary::
:nosignatures:
INVALID_SHIFT_VALUE
NEGATIVE_SHIFT_ERROR
......
......@@ -7,7 +7,7 @@ aria.core.Cluster module
.. currentmodule:: aria.core.Cluster
.. automodule:: aria.core.Cluster
:members: Clustering, ClusteringSettings, ClusteringXMLPickler
:members: Clustering, ClusteringSettings, ClusteringXMLPickler, NO
:undoc-members:
:show-inheritance:
:member-order: bysource
......@@ -24,6 +24,13 @@ Classes:
ClusteringSettings
ClusteringXMLPickler
Data:
.. autosummary::
:nosignatures:
NO
......
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