JuDFTteam · PhilippRue · Apr 15, 2020 · Apr 15, 2020 · Apr 15, 2020 · Apr 15, 2020
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,49 @@
+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: 3.6
+      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
+  - pip install -e .[testing]
+script:
+  # refresh entry points
+  - reentry scan
+  # run tests
+  - cd tests; pytest --cov-report=term-missing --cov=aiida_jutools -sv .
+after_success:
+  - pip install codecov
+  - codecov
diff --git a/aiida_jutools/structure_analyzer.py b/aiida_jutools/structure_analyzer.py
@@ -37,7 +37,7 @@
 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
@@ -48,7 +48,7 @@
 # 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
@@ -1 +1,10 @@
-aiida-core>0.9.0
+aiida-core
+masci-tools
+aiida-kkr
+numpy
+scipy
+pycifrw
+pymatgen
+spglib
+pandas
+humanfriendly
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -232,7 +232,7 @@
 #html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'aiida-jutoolsdoc'
+htmlhelp_basename = 'aiida-jutools-doc'
 
 # -- Options for LaTeX output --------------------------------------------------
 
@@ -301,49 +301,6 @@
     configuration.BACKEND = "django"
     configuration.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)
-
 
 # -- Options for manual page output --------------------------------------------
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,6 +1,6 @@
-#########################################
+######################################################################
 `AiiDA`_ helper tools used by the aiida-plugins for the `juDFT`_ codes
-#########################################
+######################################################################
 
 .. image:: images/AiiDA_transparent_logo.png
     :width: 40%

diff --git a/docs/source/module_guide/index.rst b/docs/source/module_guide/index.rst
@@ -4,5 +4,53 @@ Modules provided with aiida-jutools (API reference)
 .. toctree::
     :maxdepth: 3
 
-    utilities
+.. 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:
 
diff --git 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
diff --git a/setup.json b/setup.json
@@ -1,19 +1,18 @@
 {
     "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",
     "download_url": "https://github.com/JuDFTteam/aiida-jutools",
     "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",
         "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",
@@ -30,12 +29,19 @@
         "numpy",
         "scipy",
         "pycifrw",
+        "pymatgen",
         "spglib",
         "pandas",
         "humanfriendly"
     ],
     "extras_require": {
-        "pre-commit": [
+        "testing": [
+            "pytest-cov",
+            "pgtest"
+        ],
+        "docs": [
+            "Sphinx",
+            "sphinx-rtd-theme"
         ]
     },
     "entry_points": {

diff --git a/tests/files/Cu_mp-30_computed.cif 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/aiida_jutools/str2aiida.py → tests/test_structure_analyzer.py b/aiida_jutools/str2aiida.py → tests/test_structure_analyzer.py
@@ -16,15 +16,11 @@
 - 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 structure_analyzer import analyze_symmetry
-from terminal_colors import *
+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.")
@@ -56,4 +52,15 @@ 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_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)
Original file line number	Diff line number	Diff line change
Expand Up		@@ -5,6 +5,3 @@ User's guide
		.. toctree::
		:maxdepth: 3

		tools