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

.gitlab-ci.yml

@@ -51,8 +51,6 @@ pages:
   artifacts:
     paths:
       - public
-  only:
-    - master
 
 cleanup_pypirc:
   stage: cleanup

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 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

docs/api/aria.aria2.rst

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

docs/api/aria.ariacns.rst

+aria.ariacns module
+===================
+
+.. automodule:: aria.ariacns
+    :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, 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
+
 
 
 

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
+
 
 
 

docs/api/aria.core.Analyser.rst

@@ -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
+
 
 
 

docs/api/aria.core.AriaPeak.rst

@@ -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
+
 
 
 

docs/api/aria.core.AriaXML.rst

@@ -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
+
 
 
 

docs/api/aria.core.Assignment.rst

@@ -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
+
 
 
 

docs/api/aria.core.AssignmentFilter.rst

@@ -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
+
 
 
 

docs/api/aria.core.Atom.rst

@@ -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
+
 
 
 

docs/api/aria.core.Chain.rst

@@ -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
+
 
 
 

docs/api/aria.core.ChemicalShiftFilter.rst

@@ -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
+
 
 
 

docs/api/aria.core.Cluster.rst

@@ -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
+