Release version 0.4 (#37)

* Set license to Apache-2.0 * Update documentation * Update current VASP version * Link to the tutorials from py4vasp * Update dependencies (dependabot alert) * Add option to read band-structure from kpoints_wan Co-authored-by: Henrique Miranda <[email protected]>
vasp-dev · Feb 17, 2022 · ff31fa7 · ff31fa7
1 parent 4505b5e
commit ff31fa7
Show file tree

Hide file tree

Showing 104 changed files with 759 additions and 153 deletions.
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -0,0 +1,178 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
diff --git a/README.md b/README.md
@@ -1,21 +1,34 @@
 # py4vasp
 
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-[![tests](https://github.com/martin-schlipf/py4vasp/actions/workflows/test.yml/badge.svg)](https://github.com/martin-schlipf/py4vasp/actions/workflows/test.yml)
+[![tests](https://github.com/vasp-dev/py4vasp/actions/workflows/test.yml/badge.svg)](https://github.com/vasp-dev/py4vasp/actions/workflows/test.yml)
+
+> Please note that this document is intended mostly for developers that want to use
+> the version of py4vasp provided on Github. If you just want to install py4vasp to
+> use it, please follow the [official documentation](https://vasp.at/py4vasp).
 
 ## Installation
 
-We use the [poetry dependency manager](https://python-poetry.org/) which takes care of all dependencies and maintains a virtual environment to check the code. If you want to test something in the virtual environment, just use e.g. ```poetry run jupyter-notebook```.
+We use the [poetry dependency manager](https://python-poetry.org/) which takes care of
+all dependencies and maintains a virtual environment to check the code. If you want to
+test something in the virtual environment, just use e.g. ```poetry run jupyter-notebook```.
 
-Using poetry installing and the code requires the following steps. The last step will test whether everything worked
+Using poetry installing and the code requires the following steps. The last step will
+test whether everything worked
 ~~~shell
 git clone [email protected]:vasp-dev/py4vasp.git
 pip install poetry
 poetry install
 poetry run pytest
 ~~~
-
-We occasionally encountered errors when installing the *mdtraj* dependency in this fashion, in particular on MacOS and Windows. If you notice the same behavior, we recommend to manage your environment with *conda* and install *py4vasp* in the following manner
+Note that this will install py4vasp into a virtual environment managed by poetry. This
+isolates the code from all other packages you have installed and makes sure that when
+you modify the code all the relevant dependencies are tracked.
+
+Occasionally, we encountered errors when installing the *mdtraj* dependency in this
+fashion, in particular on MacOS and Windows. If you notice the same behavior, we
+recommend to manage your environment with *conda* and install *py4vasp* in the
+following manner
 ~~~shell
 git clone [email protected]:vasp-dev/py4vasp.git
 conda create --name py4vasp-env python=3.8
@@ -29,13 +42,22 @@ poetry run pytest
 
 ## Code style
 
-Code style is enforced, but is not something the developer should spend time on, so we decided on using the black formatter. Just run ```black .``` before committing the code.
+Code style is enforced, but is not something the developer should spend time on, so we
+decided on using the black formatter. Please run ```black .``` before committing the code.
+
+## Contributing to py4vasp
 
-## Development workflow
+We welcome contributions to py4vasp. To improve the code please follow this workflow
 
-* Create an issue for the bugfix or feature you are working on
-* Create a branch prefixing it with the number of the issue
-* Implement the bugfix or feature on the branch adding tests to check it
-* Create a pull request and link it to the issue it resolves
+* Create an issue for the bugfix or feature you plan to work on, this gives the option
+  to provide some input before work is invested.
+* Implement your work in a fork of the repository and create a pull request for it.
+  Please make sure to test your code thoroughly and commit the tests in the pull
+  request in the tests directory.
+* In the message to your merge request mention the issue the code attempts to solve.
+* We will try to include your merge request rapidly when all the tests pass and your
+  code is covered by tests.
 
-A typical pull request should have up to approximately 200 lines of code otherwise reviewing the changes gets unwieldy.
+Please limit the size of a the pull request to approximately 200 lines of code
+otherwise reviewing the changes gets unwieldy. Prefer splitting the work into
+multiple smaller chunks if necessary.
diff --git a/docs/calculation.rst b/docs/calculation.rst
@@ -0,0 +1,7 @@
+calculation
+===========
+
+.. automodule:: py4vasp.calculation
+
+.. autoclass:: py4vasp.calculation.Calculation
+  :members:
diff --git a/docs/calculation_api.rst b/docs/calculation_api.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -18,19 +18,20 @@
 # -- Project information -----------------------------------------------------
 
 project = "py4vasp"
-copyright = "2020, Vasp Software GmbH"
+copyright = "2022, Vasp Software GmbH"
 author = "Vasp Software GmbH"
 
 # The full version, including alpha/beta/rc tags
-release = "0.2"
+release = "0.4.0"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon"]
+extensions = ["sphinx.ext.napoleon", "sphinx_automodapi.automodapi"]
+automodapi_inheritance_diagram = False
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -45,8 +46,16 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
-html_theme = "nature"
+
+# default theme
+# html_theme = "nature"
+
+# a minimal theme for the website
+html_theme = "basic"
+html_show_sphinx = False
+html_show_copyright = False
+html_domain_indices = False
+html_use_index = False
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

diff --git a/docs/control.rst b/docs/control.rst
@@ -0,0 +1,4 @@
+control
+=======
+
+.. automodapi:: py4vasp.control
diff --git a/docs/control_api.rst b/docs/control_api.rst
diff --git a/docs/data.rst b/docs/data.rst
@@ -0,0 +1,5 @@
+data
+====
+
+.. automodapi:: py4vasp.data
+  :inherited-members:
diff --git a/docs/data_api.rst b/docs/data_api.rst
diff --git a/docs/exceptions.rst b/docs/exceptions.rst
@@ -0,0 +1,4 @@
+exceptions
+==========
+
+.. automodapi:: py4vasp.exceptions
diff --git a/docs/exceptions_api.rst b/docs/exceptions_api.rst