Update readme

.binder/postBuild

@@ -1,20 +1,20 @@
 # pip install main
 pip install --no-deps .
-# Note: This produces build and pyiron_module_template.egg-info directories
+# Note: This produces build and elaston.egg-info directories
 
 # clean up
 if [ -d "notebooks" ]; then
     mv notebooks/* .
 fi
-if [ -d "${HOME}/pyiron_module_template" ]; then
+if [ -d "${HOME}/elaston" ]; then
     rm -r   ${HOME}/.binder \
             ${HOME}/.ci_support \
             ${HOME}/.github \
             ${HOME}/build \
             ${HOME}/docs \
             ${HOME}/notebooks \
-            ${HOME}/pyiron_module_template \
-            ${HOME}/pyiron_module_template.egg-info \
+            ${HOME}/elaston \
+            ${HOME}/elaston.egg-info \
             ${HOME}/tests \
             ${HOME}/.gitattributes \
             ${HOME}/.gitignore \

.coveragerc

@@ -1,5 +1,5 @@
 # .coveragerc to control coverage.py
 [run]
-source = pyiron_module_template
-omit = pyiron_module_template/_version.py
+source = elaston
+omit = elaston/_version.py
 concurrency = multiprocessing

.gitattributes

@@ -1 +1 @@
-pyiron_module_template/_version.py export-subst
+elaston/_version.py export-subst

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,6 +1,6 @@
 ---
 name: Bug report
-about: Create a bug report to help us eliminate issues and improve pyiron_module_template
+about: Create a bug report to help us eliminate issues and improve elaston
 title: ''
 labels: bug
 assignees: ''

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,6 +1,6 @@
 ---
 name: Feature request
-about: Make a suggestion for a new feature or a change to pyiron_module_template
+about: Make a suggestion for a new feature or a change to elaston
 title: ''
 labels: enhancement
 assignees: ''
@@ -13,7 +13,7 @@ assignees: ''
 
 **Detailed Description**
 
-<!--Please explain how you would like to see pyiron_module_template enhanced, what feature(s) you are looking for, what specific problems this will solve.-->
+<!--Please explain how you would like to see elaston enhanced, what feature(s) you are looking for, what specific problems this will solve.-->
 
 **Further Information, Files, and Links**
 

docs/README.md

@@ -1,112 +1,63 @@
-# pyiron_module_template
-
-## Overview
-
-This repository is a template for new pyiron modules similar to the existing modules of the 
-pyiron framework, e.g. 
-[pyiron_workflow](https://github.com/pyiron/pyiron_workflow),
-[pyiron_ontology](https://github.com/pyiron/pyiron_ontology),
-etc.
-
-Within this repository, the new module is called `pyiron_module_template` which should be renamed to `pyiron_IntendedModuleName`. 
-This can be easily achieved by modifying and running `bash ./update_module_name.sh` script.
-
-The licence is free to choose, but as a default the BSD3 licence packed here.
-
-## Continuous Integration
-
-We collect all files relevant for the continuous integration (CI) pipelines in `.ci_support`, 
-while the actual CI workflows are handled by GitHub and stored in `.github`.
-If you are cloning this template *inside* the pyiron GitHub organization, the full CI should work out-of-the-box by calling reusable workflows from [pyiron/actions](github.com/pyiron/actions) and inheriting organization-wide secrets.
-Otherwise, you will either need to modify the CI workflow files, or give your repository the following secrets:
-- `DEPENDABOT_WORKFLOW_TOKEN` (GitHub token for an account that has permissions to your repository -- needs to differ from the default `github_token` already available though! In pyiron we have a special [@pyiron_runner account](https://github.com/pyiron-runner) for this purpose.)
-- `PYPI_PASSWORD` (Token generated on PyPi to give access to your account there)
-- `CODACY_PROJECT_TOKEN` (Token generated on Codacy to give access to your account there)
-
-The default CI setup from [pyiron/actions](github.com/pyiron/actions) makes some assumptions about your directory structure.
-The most important one is that your environment should be specified in `.ci_support/environment.yml`.
-There is a base environment there already, giving dependence on `pyiron_base`.
-The CI will automatically keep environment files read by readthedocs (which will look at `.readthedocs.yml`) and MyBinder (which looks in `.binder`) up-to-date based on this environment file.
-
-In case you need extra environment files for some setups, you can modify the workflows in `.github/workflows`, which accept input variables for the docs, tests, and notebooks environments.
-For example, it's typically good to not make your project depend on the `lammps` package, since this is not available for windows.
-However, you might want to give some demo notebooks that run on MyBinder (a linux environment) and use LAMMPS calculations.
-In this case, you could add a new file `.ci_support/environment-notebooks.yml`, and then edit `.github/workflows/push-pull.yml` so that instead of reading 
-
-```yaml
-jobs:
-  pyiron:
-    uses: pyiron/actions/.github/workflows/[email protected]
-    secrets: inherit
-    # All the environment files variables point to .ci_support/environment.yml by default
-```
+# Elaston
 
-It instead reads
+Elaston is a simple and lightweight module for linear elasticity calculations.
 
-```yaml
-jobs:
-  pyiron:
-    uses: pyiron/actions/.github/workflows/[email protected]
-    secrets: inherit
-    with:
-      notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml
-```
+## Installation
 
-Where `.ci_support/environment-notebooks.yml` looks like:
+We will offer pip and conda at some point. For now, you can install the package by cloning the repository and running the following command in the root directory:
 
-```yaml
-channels:
-  - conda-forge
-dependencies:
-  - lammps
+```bash
+pip install .
 ```
 
-### Dependencies
+## Features
 
-The CI for making new releases expects all the `pyproject.toml` dependencies to be fully specified with `==` and the conda dependencies to have their versions specified by `=`, i.e. precisely specifying the version the code here is intended to run on.
-At release time, these dependencies can be relaxed so that new users installing your code may have access to a wider variety of environment possibilities.
-For exact details on this relaxation, check documentation in the [centralized CI](https://github.com/pyiron/actions).
+- Calculation of elastic constants
+- Stress strain field around dislocations using anisotropic elasticity
+- Stress strain field around point defects
 
-### Label-based CI
 
-Some CI triggers when labels get applied to a PR. 
-In a new repository, you will need to define these labels:
-- `format_black`: Runs black analyis and creates a bot-generated commit to fix any format violations
-- `run_CodeQL`: Runs the external CodeQL analysis (expensive, only do at the end)
-- `run_coverage`: Run all the tests in `tests` and use coveralls to generate a coverage report (also expensive, only run near the end of your PR)
+## Usage
 
-## Documentation
+Examples I: Get bulk modulus from the elastic tensor:
 
-You should modify this README to reflect the purpose of your new package.
-You can look at the other pyiron modules to get a hint for what sort of information to include, and how to link badges at the head of your README file.
+```python
+from elaston import LinearElasticity
 
-At a minimum, we suggest creating a meaningful example notebook in the `notebooks/` directory and creating a MyBinder badge so that people can quickly and easily explore your work.
+medium = LinearElasticity(elastic_tensor)
+print(medium.bulk_modulus)
+```
 
-You can also edit the docs for your package by modifying `docs/index.rst`.
-By default, this README is used as the landing page, and a simple API section is automatically generated.
 
-## Tests
+Example II: Get strain field around a point defect:
 
-There is space for "benchmark", "integration", and "unit" tests in the `tests/` directory, with dummy tests for each.
-These are run by the default CI, so modify them to suit your needs.
+```python
+import numpy as np
+medium = LinearElasticity(elastic_tensor)
+random_positions = np.random.random((10, 3))-0.5
+dipole_tensor = np.eye(3)
+print(medium.get_point_defect_strain(random_positions, dipole_tensor))
+```
 
-Additionally, the standard CI will attempt to execute all notebooks in the `notebooks/` directory.
-See [`pyiron/actions`](https://github.com/pyiron/actions) and the reusable workflows there to learn about modifying the environment for the CI, e.g. to use a different env for notebook runs than for the tests in `tests/`.
 
-Finally, `tests/integration/test_readme.py` shows how example code in the documentation gets tested against its claimed output.
-E.g. if you change this:
+Example III: Get stress field around a dislocation:
 
 ```python
->>> print(2 + 2)
-4
-
+import numpy as np
+medium = LinearElasticity(elastic_tensor)
+random_positions = np.random.random((10, 3))-0.5
+burgers_vector = np.array([0, 0, 1])
+print(medium.get_dislocation_stress(random_positions, burgers_vector))
 ```
 
-To read `5` instead, those tests should fail.
-
-## Publishing your package
-
-If you are inside the pyiron organization or have your own `PYPI_PASSWORD` secret configured, your package will be published on PyPI automatically when you make a new "release" on GitHub -- *as long as* that tag matches the pattern specified in `setup.cfg`; by default any tag that `pyiron_module_template-`, where `pyiron_module_template` is replaced with the name of your module. We recommend using semantic versioning so that your first release looks like `pyiron_module_template-0.0.1`.
+Example IV: Estimate the distance between partial dislocations:
 
-Releasing your package on Conda-Forge is slightly more involved, but not too hard (at least for pure python packages).
-See [conda-forge/staged-recipes](https://github.com/conda-forge/staged-recipes) for how to publish it there.
+```python
+medium = LinearElasticity(elastic_tensor)
+partial_one = np.array([-0.5, 0, np.sqrt(3)/2])*lattice_constant
+partial_two = np.array([0.5, 0, np.sqrt(3)/2])*lattice_constant
+distance = 100
+stress_one = medium.get_dislocation_stress([0, distance, 0], partial_one)
+print('Choose `distance` in the way that the value below corresponds to SFE')
+medium.get_dislocation_force(stress_one, [0, 1, 0], partial_two)
+```

docs/index.rst

@@ -1,4 +1,4 @@
-.. pyiron_module_template documentation master file
+.. elaston documentation master file
 
 .. _index: