From 8bee3fedd3699816cc3f67ad2bc6fbc33bb93595 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 16:33:53 +0200 Subject: [PATCH 01/15] Make dos compilation work --- aiida_jutools/__init__.py | 1 + aiida_jutools/structure_analyzer.py | 4 +- docs/requirements_for_rtd.txt | 2 +- docs/source/conf.py | 77 +++++------------------------ docs/source/index.rst | 6 +-- docs/source/module_guide/index.rst | 9 ++-- docs/source/module_guide/tools.rst | 15 ------ docs/source/user_guide/index.rst | 3 -- docs/source/user_guide/tools.rst | 4 -- setup.json | 10 ++-- 10 files changed, 32 insertions(+), 99 deletions(-) delete mode 100644 docs/source/module_guide/tools.rst delete mode 100644 docs/source/user_guide/tools.rst diff --git a/aiida_jutools/__init__.py b/aiida_jutools/__init__.py index e69de29..f102a9c 100644 --- a/aiida_jutools/__init__.py +++ b/aiida_jutools/__init__.py @@ -0,0 +1 @@ +__version__ = "0.0.1" diff --git a/aiida_jutools/structure_analyzer.py b/aiida_jutools/structure_analyzer.py index b3b5f60..a4e1461 100644 --- a/aiida_jutools/structure_analyzer.py +++ b/aiida_jutools/structure_analyzer.py @@ -26,7 +26,7 @@ import spglib # local imports -from terminal_colors import * +from .terminal_colors import * # CSQ color for sequence # CDB color for structure database # CRC color for recipe @@ -37,7 +37,7 @@ # CER color for error messages # COK color for OK messages # CIN color for info messages -from ptable import ptable +from .ptable import ptable __copyright__ = (u"Copyright (c), 2019-2020, Forschungszentrum Jülich GmbH, " "IAS-1/PGI-1, Germany. All rights reserved.") diff --git a/docs/requirements_for_rtd.txt b/docs/requirements_for_rtd.txt index e273837..93fd4bf 100644 --- a/docs/requirements_for_rtd.txt +++ b/docs/requirements_for_rtd.txt @@ -1 +1 @@ -aiida-core>0.9.0 +aiida-core~=1.0.0 diff --git a/docs/source/conf.py b/docs/source/conf.py index 44f262e..c12c909 100755 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -22,14 +22,13 @@ os.environ['DJANGO_SETTINGS_MODULE'] = 'rtd_settings' import aiida -from aiida.backends import settings # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. #sys.path.append(os.path.abspath('../')) #sys.path.append(os.path.abspath('../../')) -import aiida_kkr +import aiida_jutools # -- General configuration ------------------------------------------------ @@ -72,7 +71,7 @@ master_doc = 'index' # General information about the project. -project = u'aiida-kkr' +project = u'aiida-jutools' copyright_first_year = 2017 copyright_owners = u"FZ Jülich GmbH, Germany" @@ -85,7 +84,7 @@ # built documents. # # The full version, including alpha/beta/rc tags. -release = aiida_kkr.__version__ +release = aiida_jutools.__version__ # The short X.Y version. version = '.'.join(release.split('.')[:2]) @@ -213,7 +212,7 @@ # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. -html_use_opensearch = 'http://aiida-kkr.readthedocs.io' +html_use_opensearch = 'http://aiida-jutools.readthedocs.io' # This is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = None @@ -233,7 +232,7 @@ #html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. -htmlhelp_basename = 'aiida-kkrdoc' +htmlhelp_basename = 'aiida-jutools-doc' # -- Options for LaTeX output -------------------------------------------------- @@ -254,7 +253,7 @@ # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ('index', 'aiida-kkr.tex', u'AiiDA-KKR documentation', + ('index', 'aiida-jutools.tex', u'AiiDA-Jutools documentation', author.replace(',',r'\and'), 'manual'), ] @@ -278,9 +277,6 @@ # If false, no module index is generated. #latex_domain_indices = True -# We set that we are in documentation mode - even for local compilation -settings.IN_DOC_MODE = True - # on_rtd is whether we are on readthedocs.org, this line of code grabbed # from docs.readthedocs.org # NOTE: it is needed to have these lines before load_profile() @@ -300,53 +296,10 @@ load_profile() else: # Back-end settings for readthedocs online documentation. - # from aiida.backends import settings - settings.IN_RT_DOC_MODE = True - settings.BACKEND = "django" - settings.AIIDADB_PROFILE = "default" - -''' -def run_apidoc(_): - """Runs sphinx-apidoc when building the documentation. - - Needs to be done in conf.py in order to include the APIdoc in the - build on readthedocs. - - See also https://github.com/rtfd/readthedocs.org/issues/1139 - """ - source_dir = os.path.abspath(os.path.dirname(__file__)) - apidoc_dir = os.path.join(source_dir, 'apidoc') - package_dir = os.path.join(source_dir, os.pardir, os.pardir) - - # In #1139, they suggest the route below, but for me this ended up - # calling sphinx-build, not sphinx-apidoc - #from sphinx.apidoc import main - #main([None, '-e', '-o', apidoc_dir, package_dir, '--force']) - - import subprocess - cmd_path = 'sphinx-apidoc' - if hasattr(sys, 'real_prefix'): # Check to see if we are in a virtualenv - # If we are, assemble the path manually - cmd_path = os.path.abspath(os.path.join(sys.prefix, 'bin', 'sphinx-apidoc')) - - options = [ - '-o', apidoc_dir, package_dir, - '--private', - '--force', - '--no-headings', - '--module-first', - '--no-toc', - '--maxdepth', '4', - ] - - # See https://stackoverflow.com/a/30144019 - env = os.environ.copy() - env["SPHINX_APIDOC_OPTIONS"] = 'members,special-members,private-members,undoc-members,show-inheritance' - subprocess.check_call([cmd_path] + options, env=env) -''' - -#def setup(app): -# app.connect('builder-inited', run_apidoc) + from aiida.manage import configuration + configuration.IN_RT_DOC_MODE = True + configuration.BACKEND = "django" + configuration.AIIDADB_PROFILE = "default" # -- Options for manual page output -------------------------------------------- @@ -354,7 +307,7 @@ def run_apidoc(_): # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - ('index', 'aiida-kkr', u'AiiDA-KKR documentation', + ('index', 'aiida-jutools', u'AiiDA-Jutools documentation', [author], 1) ] @@ -368,7 +321,7 @@ def run_apidoc(_): # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - ('index', 'aiida-kkr', u'AiiDA-KKR documentation', + ('index', 'aiida-jutools', u'AiiDA-Ju documentation', author, 'aiida', 'KKR pluginf for Aiida framework', 'Miscellaneous'), ] @@ -433,12 +386,6 @@ def run_apidoc(_): # We should ignore any python built-in exception, for instance nitpick_ignore = [] -for line in open('nitpick-exceptions'): - if line.strip() == "" or line.startswith("#"): - continue - dtype, target = line.split(None, 1) - target = target.strip() - nitpick_ignore.append((dtype, target)) nitpick_ignore = [ ('py:exc', 'ArithmeticError'), ('py:exc', 'AssertionError'), diff --git a/docs/source/index.rst b/docs/source/index.rst index 37dcc88..7360927 100755 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,6 +1,6 @@ -######################################### +####################################################################### `AiiDA`_ helper tools used byt the aiida-plugins for the `juDFT`_ codes -######################################### +####################################################################### .. image:: images/AiiDA_transparent_logo.png :width: 40% @@ -33,7 +33,7 @@ User's guide user_guide/index Modules provided with aiida-jutools (API reference) -+++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++ .. toctree:: :maxdepth: 4 diff --git a/docs/source/module_guide/index.rst b/docs/source/module_guide/index.rst index 587a11c..61d1453 100644 --- a/docs/source/module_guide/index.rst +++ b/docs/source/module_guide/index.rst @@ -1,8 +1,11 @@ -Modules provided with aiida-kkr (API reference) -=============================================== +Modules provided with aiida-jutools (API reference) +=================================================== .. toctree:: :maxdepth: 3 - tools +.. automodule:: aiida_jutools.structure_analyzer + :members: + :private-members: + :special-members: diff --git a/docs/source/module_guide/tools.rst b/docs/source/module_guide/tools.rst deleted file mode 100644 index 67900c6..0000000 --- a/docs/source/module_guide/tools.rst +++ /dev/null @@ -1,15 +0,0 @@ -Tools -+++++ - -.. toctree:: - :maxdepth: 2 - -Here the tools provided by ``aiida_kkr`` are described. - -Common (work)functions that need aiida --------------------------------------- -.. automodule:: aiida_kkr.tools.common_workfunctions - :members: - :private-members: - :special-members: - diff --git a/docs/source/user_guide/index.rst b/docs/source/user_guide/index.rst index 34e1287..5d065a7 100644 --- a/docs/source/user_guide/index.rst +++ b/docs/source/user_guide/index.rst @@ -5,6 +5,3 @@ User's guide .. toctree:: :maxdepth: 3 - tools - - diff --git a/docs/source/user_guide/tools.rst b/docs/source/user_guide/tools.rst deleted file mode 100644 index 3980ff6..0000000 --- a/docs/source/user_guide/tools.rst +++ /dev/null @@ -1,4 +0,0 @@ -===== -Tools -===== - diff --git a/setup.json b/setup.json index e00848a..e55543b 100644 --- a/setup.json +++ b/setup.json @@ -1,6 +1,6 @@ { "name": "aiida-jutools", - "author": "JuDFTteam, Philipp Rüßmann", + "author": "JuDFTteam", "author_email": "p.ruessmann@fz-juelich.de", "description": "AiiDA helper for Jülich AiiDA plugins", "url": "https://github.com/JuDFTteam/aiida-jutools", @@ -8,7 +8,6 @@ "license": "MIT", "classifiers": [ "License :: OSI Approved :: MIT License", - "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", @@ -24,9 +23,14 @@ "version": "0.0.1", "reentry_register": true, "install_requires": [ + "aiida-core~=1.1.1", + "pymatgen", + "PyCifRW" ], "extras_require": { - "pre-commit": [ + "docs": [ + "sphinx", + "sphinx-rtd-theme" ] }, "entry_points": { From d83170d182df5695a78e9475c08f05af2358b070 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 16:37:55 +0200 Subject: [PATCH 02/15] Add travis settings --- .travis.yml | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..b94c67e --- /dev/null +++ b/.travis.yml @@ -0,0 +1,23 @@ +dist: xenial +language: python +matrix: + # mark build as complete as soon as the versions that may not fail is finished + fast_finish: true + include: + - python: 3.4 + - python: 3.5 + - python: 3.6 + - python: 3.7 + - python: 3.8 +cache: pip +install: # python installations + - pip install -U pip wheel setuptools + - pip install -U pytest + - pip install -e . + - pip install codecov +script: + - pytest -sv . +after_success: + - codecov +git: + depth: 3 From 2ad3f470937b8673058f346feadbb95f9734a060 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 16:49:37 +0200 Subject: [PATCH 03/15] prepare first test --- setup.json | 3 +++ .../str2aiida.py => tests/test_structure_analyzer.py | 8 +++++--- 2 files changed, 8 insertions(+), 3 deletions(-) rename aiida_jutools/str2aiida.py => tests/test_structure_analyzer.py (89%) diff --git a/setup.json b/setup.json index e55543b..f5e2475 100644 --- a/setup.json +++ b/setup.json @@ -28,6 +28,9 @@ "PyCifRW" ], "extras_require": { + "testing": [ + "pytest" + ], "docs": [ "sphinx", "sphinx-rtd-theme" diff --git a/aiida_jutools/str2aiida.py b/tests/test_structure_analyzer.py similarity index 89% rename from aiida_jutools/str2aiida.py rename to tests/test_structure_analyzer.py index 0bd1f56..32f15a9 100644 --- a/aiida_jutools/str2aiida.py +++ b/tests/test_structure_analyzer.py @@ -11,8 +11,8 @@ from aiida import load_profile load_profile() -from structure_analyzer import analyze_symmetry -from terminal_colors import * +from aiida_jutools.structure_analyzer import analyze_symmetry +from aiida_jutools.terminal_colors import * from pprint import pprint __copyright__ = (u"Copyright (c), 2019-2020, Forschungszentrum Jülich GmbH, " @@ -45,4 +45,6 @@ def cif2astr(cifpath): print('\n'+'extras:'+'\n') pprint(structure['aiida_structure_conventional'].extras, width=256) -cif2astr('/path/to/cif/file.cif') + +def test_cif2astr(aiida_env): + cif2astr('files/Cu_mp-30_computed.cif') From 655d64449665de0a2a83611b1c4b3cbe0542bbf7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 17:03:08 +0200 Subject: [PATCH 04/15] update requirements for rtd build --- .travis.yml | 15 +++++++-------- docs/requirements_for_rtd.txt | 1 + setup.json | 2 +- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.travis.yml b/.travis.yml index b94c67e..957c1c4 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,23 +1,22 @@ dist: xenial language: python +git: + depth: 3 +cache: pip matrix: # mark build as complete as soon as the versions that may not fail is finished fast_finish: true include: - - python: 3.4 - python: 3.5 - python: 3.6 - python: 3.7 - python: 3.8 -cache: pip install: # python installations - pip install -U pip wheel setuptools - pip install -U pytest - pip install -e . - pip install codecov -script: - - pytest -sv . -after_success: - - codecov -git: - depth: 3 +#script: +# - pytest -sv . +#after_success: +# - codecov diff --git a/docs/requirements_for_rtd.txt b/docs/requirements_for_rtd.txt index 93fd4bf..39aacc2 100644 --- a/docs/requirements_for_rtd.txt +++ b/docs/requirements_for_rtd.txt @@ -1 +1,2 @@ aiida-core~=1.0.0 +numpy~=1.17 diff --git a/setup.json b/setup.json index f5e2475..9d32d35 100644 --- a/setup.json +++ b/setup.json @@ -9,10 +9,10 @@ "classifiers": [ "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", "Development Status :: 4 - Beta", "Environment :: Plugins", "Intended Audience :: Science/Research", From 3e4a759d63ab546300ebadbcc353b1a697399320 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 17:19:04 +0200 Subject: [PATCH 05/15] Add Cu test (import cif from materialsproject) --- setup.json | 3 ++- tests/files/Cu_mp-30_computed.cif | 27 +++++++++++++++++++++++++++ tests/test_structure_analyzer.py | 21 +++++++++++++-------- 3 files changed, 42 insertions(+), 9 deletions(-) create mode 100644 tests/files/Cu_mp-30_computed.cif mode change 100644 => 100755 tests/test_structure_analyzer.py diff --git a/setup.json b/setup.json index 9d32d35..fc36331 100644 --- a/setup.json +++ b/setup.json @@ -29,7 +29,8 @@ ], "extras_require": { "testing": [ - "pytest" + "pytest", + "pgtest" ], "docs": [ "sphinx", diff --git a/tests/files/Cu_mp-30_computed.cif b/tests/files/Cu_mp-30_computed.cif new file mode 100644 index 0000000..622465c --- /dev/null +++ b/tests/files/Cu_mp-30_computed.cif @@ -0,0 +1,27 @@ +# generated using pymatgen +data_Cu +_symmetry_space_group_name_H-M 'P 1' +_cell_length_a 2.56061937 +_cell_length_b 2.56061937 +_cell_length_c 2.56061937 +_cell_angle_alpha 60.00000000 +_cell_angle_beta 60.00000000 +_cell_angle_gamma 60.00000000 +_symmetry_Int_Tables_number 1 +_chemical_formula_structural Cu +_chemical_formula_sum Cu1 +_cell_volume 11.87189593 +_cell_formula_units_Z 1 +loop_ + _symmetry_equiv_pos_site_id + _symmetry_equiv_pos_as_xyz + 1 'x, y, z' +loop_ + _atom_site_type_symbol + _atom_site_label + _atom_site_symmetry_multiplicity + _atom_site_fract_x + _atom_site_fract_y + _atom_site_fract_z + _atom_site_occupancy + Cu Cu0 1 0.000000 -0.000000 0.000000 1 diff --git a/tests/test_structure_analyzer.py b/tests/test_structure_analyzer.py old mode 100644 new mode 100755 index 32f15a9..a046ed7 --- a/tests/test_structure_analyzer.py +++ b/tests/test_structure_analyzer.py @@ -5,15 +5,11 @@ - apart from aiida, pymatgen and PyCifRW packages are needed to use > analyze_symmetry < """ -import sys - -# aiida imports -from aiida import load_profile -load_profile() - +from aiida.manage.tests.pytest_fixtures import aiida_profile from aiida_jutools.structure_analyzer import analyze_symmetry from aiida_jutools.terminal_colors import * from pprint import pprint +import pathlib __copyright__ = (u"Copyright (c), 2019-2020, Forschungszentrum Jülich GmbH, " "IAS-1/PGI-1, Germany. All rights reserved.") @@ -46,5 +42,14 @@ def cif2astr(cifpath): pprint(structure['aiida_structure_conventional'].extras, width=256) -def test_cif2astr(aiida_env): - cif2astr('files/Cu_mp-30_computed.cif') +def test_cif2astr(aiida_profile): + cifpath = pathlib.Path('files/Cu_mp-30_computed.cif') + cif_abspath = str(cifpath.absolute()) + print(cif_abspath) + cif2astr(cif_abspath) + + +if __name__=='__main__': + from aiida import load_profile + load_profile() + test_cif2astr(None) From 9dd74b5ff48dc3622f42c73c13b8c322a07d4022 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 17:29:24 +0200 Subject: [PATCH 06/15] Add requirements for docs install --- .travis.yml | 8 ++++---- docs/requirements_for_rtd.txt | 2 ++ 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 957c1c4..8e1d938 100644 --- a/.travis.yml +++ b/.travis.yml @@ -16,7 +16,7 @@ install: # python installations - pip install -U pytest - pip install -e . - pip install codecov -#script: -# - pytest -sv . -#after_success: -# - codecov +script: + - pytest -sv . +after_success: + - codecov diff --git a/docs/requirements_for_rtd.txt b/docs/requirements_for_rtd.txt index 39aacc2..f6fc61e 100644 --- a/docs/requirements_for_rtd.txt +++ b/docs/requirements_for_rtd.txt @@ -1,2 +1,4 @@ aiida-core~=1.0.0 numpy~=1.17 +pymatgen +PyCifRW From 0d5ac5cc38833b44d93cac3d35c3ca84eee794c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 17:36:05 +0200 Subject: [PATCH 07/15] Do reentry scan after installation --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 8e1d938..7ce59af 100644 --- a/.travis.yml +++ b/.travis.yml @@ -16,6 +16,7 @@ install: # python installations - pip install -U pytest - pip install -e . - pip install codecov + - reentry scan script: - pytest -sv . after_success: From 830930dbb22a446cb0f9ffb3c9eff26539ca6028 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 17:41:51 +0200 Subject: [PATCH 08/15] Update installtion --- .travis.yml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 7ce59af..648a2ea 100644 --- a/.travis.yml +++ b/.travis.yml @@ -13,11 +13,13 @@ matrix: - python: 3.8 install: # python installations - pip install -U pip wheel setuptools - - pip install -U pytest - - pip install -e . - - pip install codecov - - reentry scan + # install package and requirements for tests + - pip install -e .[testing] script: + # refresh entry points + - reentry scan + # run tests - pytest -sv . after_success: + - pip install codecov - codecov From 3c35585593094a9943b654a5c4f2a0045a4d70b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 17:44:47 +0200 Subject: [PATCH 09/15] Go into tests dir for running tests --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 648a2ea..65ade64 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,7 +19,7 @@ script: # refresh entry points - reentry scan # run tests - - pytest -sv . + - cd tests; pytest --cov -sv . after_success: - pip install codecov - codecov From c0fe039223fcb8ef3e69fb1b51ed13342ec9903a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 17:48:35 +0200 Subject: [PATCH 10/15] Update pytest call --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 65ade64..988eeef 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,7 +19,7 @@ script: # refresh entry points - reentry scan # run tests - - cd tests; pytest --cov -sv . + - cd tests; pytest --cov-report=term-missing --cov=aiida_jutools -sv . after_success: - pip install codecov - codecov From aad6e337724ec58d6a12ab42fe672fe1b7a774a1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 17:53:07 +0200 Subject: [PATCH 11/15] CHange to pytest-cov --- setup.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.json b/setup.json index fc36331..a0f5ac6 100644 --- a/setup.json +++ b/setup.json @@ -29,11 +29,11 @@ ], "extras_require": { "testing": [ - "pytest", + "pytest-cov", "pgtest" ], "docs": [ - "sphinx", + "Sphinx", "sphinx-rtd-theme" ] }, From 496936755c365829af5c497a3af358ebe1cf13d9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 15 Apr 2020 17:56:51 +0200 Subject: [PATCH 12/15] add rabbitmq and postgres --- .travis.yml | 28 ++++++++++++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 988eeef..700ba0e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,4 +1,3 @@ -dist: xenial language: python git: depth: 3 @@ -7,10 +6,35 @@ matrix: # mark build as complete as soon as the versions that may not fail is finished fast_finish: true include: - - python: 3.5 - python: 3.6 + dist: trusty + addons: + postgresql: '9.5' - python: 3.7 + dist: xenial + #env: NO_RMQ='t' + addons: + postgresql: '9.5' + apt: + packages: + - rabbitmq-server - python: 3.8 + dist: xenial + addons: + postgresql: '9.5' + apt: + packages: + - rabbitmq-server +services: + - postgresql + - rabbitmq +before_install: + # Now we install the needed dependencies + - sudo apt-get install locate + - sudo service postgresql stop + - sudo apt-get remove postgresql + - sudo apt-get install postgresql-9.5 + - sudo updatedb install: # python installations - pip install -U pip wheel setuptools # install package and requirements for tests From 903048f8da255bae736b7e2be57a8f9d3b57a9cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 17 Feb 2021 11:00:48 +0100 Subject: [PATCH 13/15] relax requirements for docs --- docs/requirements_for_rtd.txt | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/docs/requirements_for_rtd.txt b/docs/requirements_for_rtd.txt index f6fc61e..d15c933 100644 --- a/docs/requirements_for_rtd.txt +++ b/docs/requirements_for_rtd.txt @@ -1,4 +1,10 @@ -aiida-core~=1.0.0 -numpy~=1.17 +aiida-core +masci-tools +aiida-kkr +numpy +scipy +pycifrw pymatgen -PyCifRW +spglib +pandas +humanfriendly From 44fbce2a80381b1f9ba893febecfe2833dd934d1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BCssmann?= Date: Wed, 17 Feb 2021 11:08:03 +0100 Subject: [PATCH 14/15] Add auto docs for modules --- docs/source/module_guide/index.rst | 45 ++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/docs/source/module_guide/index.rst b/docs/source/module_guide/index.rst index 61d1453..736759f 100644 --- a/docs/source/module_guide/index.rst +++ b/docs/source/module_guide/index.rst @@ -4,8 +4,53 @@ Modules provided with aiida-jutools (API reference) .. toctree:: :maxdepth: 3 +.. automodule:: aiida_jutools.ptable + :members: + :private-members: + :special-members: + +.. automodule:: aiida_jutools.terminal_colors + :members: + :private-members: + :special-members: + +.. automodule:: aiida_jutools.util_computer + :members: + :private-members: + :special-members: + +.. automodule:: aiida_jutools.util_group + :members: + :private-members: + :special-members: + +.. automodule:: aiida_jutools.util_node + :members: + :private-members: + :special-members: + .. automodule:: aiida_jutools.structure_analyzer :members: :private-members: :special-members: +.. automodule:: aiida_jutools.util_code + :members: + :private-members: + :special-members: + +.. automodule:: aiida_jutools.util_data + :members: + :private-members: + :special-members: + +.. automodule:: aiida_jutools.util_kkr + :members: + :private-members: + :special-members: + +.. automodule:: aiida_jutools.util_process + :members: + :private-members: + :special-members: + From 8b7c0b5762992093ee1ce40f6cd96526fd01daab Mon Sep 17 00:00:00 2001 From: johannes wasmer Date: Wed, 26 May 2021 16:57:20 +0200 Subject: [PATCH 15/15] Merge branch 'develop' into fix_docs