easyscience · AndrewSazonov · Oct 21, 2024 · Apr 11, 2024 · Apr 11, 2024 · Apr 11, 2024
diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml
@@ -12,8 +12,8 @@
 
 name: CI using pip
 
-# Trigger the workflow on push or pull request
-on: [push, pull_request]
+# Trigger the workflow on push, pull request and manual trigger
+on: [push, pull_request, workflow_call]
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
@@ -58,10 +58,10 @@ jobs:
       run: |
         pip install -e '.[dev]'
 
-    # - name: Test with tox
-    #   run: |
-    #     pip install tox tox-gh-actions coverage
-    #     tox
+    - name: Test with tox
+      run: |
+        pip install tox tox-gh-actions coverage
+        tox
 
     # - name: Upload coverage
     #   uses: codecov/codecov-action@v3

diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,3 +1,88 @@
-## Contributing
-We absolutely welcome contributions. **easyDiffractionLib** is maintained by the ESS and on a volunteer basis and thus we need to foster a community that can support user questions and develop new features to make this software a useful tool for all users while encouraging every member of the community to share their ideas.
+# Contributing
 
+When contributing to the EasyDiffractionLib repository, please first discuss the change you wish to make via issue,
+email, or any other method with the owners of this repository before making a change. 
+
+Please note we have a code of conduct, please follow it in all your interactions with the project.
+
+## Pull Request Process
+
+1. Ensure any install or build dependencies are removed before the end of the layer when doing a 
+   build.
+2. Update the README.md with details of changes to the interface, this includes new environment 
+   variables, exposed ports, useful file locations and container parameters.
+3. Increase the version numbers in any examples files and the README.md to the new version that this
+   Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).
+4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you 
+   do not have permission to do that, you may request the second reviewer to merge it for you.
+
+## Code of Conduct
+
+### Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+### Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+
+Examples of unacceptable behavior by participants include:
+
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+### Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+### Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+### Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at suport@easydiffraction.org. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+### Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/
diff --git a/README.md b/README.md
@@ -1,26 +1,25 @@
 # [![Unit Tests][20]][21] ![Release][31] [![Downloads][70]][71] [![Lines of code][81]](<>) [![Total lines][80]](<>) [![Files][82]](<>) [![License][50]][51] [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/easyScience/easyDiffractionLib/develop)
 
-
 [![](http://github-actions.40ants.com/easyScience/easyDiffractionLib/matrix.svg)](https://github.com/easyScience/easyDiffractionLib/actions)
 
 <img height="80"><img src="https://raw.githubusercontent.com/easyScience/easyDiffractionApp/master/resources/images/ed_logo.svg" height="65">
 
-**easydiffractionLib** is a Python library which provides:
+**Easydiffraction** is a Python library which provides:
 * Scripting interface to simulate and analyse neutron diffraction patterns.
 * Multiple optimization algorithms to minimize models to experimental data: [Lmfit](https://lmfit.github.io/lmfit-py/), [Bumps](https://github.com/bumps/bumps) and [DFO_LS](https://github.com/numericalalgorithmsgroup/dfols).
 * Multiple calculation engines: [CrysPy](https://github.com/ikibalin/cryspy), [CrysFML](https://www.ill.eu/sites/fullprof/php/programs24b7.html?pagina=Crysfml).
 
-**easydiffractionLib** is the foundation of [**easyDiffraction**](https://github.com/easyScience/easyDiffraction), an intuitive application which endeavors simplifying and accelerating the analysis of diffraction experiments.
+**Easydiffraction** library is the foundation of [**EasyDiffraction** application](https://github.com/easyscience/easydiffractionapp), an intuitive application which endeavors simplifying and accelerating the analysis of diffraction experiments.
 
 ## Getting Started
 
-### Install easyDiffractionLib
+### Install EasyDiffraction python library
 
-Currently **easyDiffractionLib** is in **alpha** and has not been released on **pypi**. Please use the alternative method given below to install **easyDiffractionLib** from our [custom Python Package Index](https://easyscience.github.io/pypi).
+Currently **easydiffraction** is in **alpha** and has not been released on **pypi**. Please use the alternative method given below to install **easydiffraction** from our GitHub repository.
 
-* Create and go to, e.g., **easyDiffraction** directory (*optional*)
+* Create and go to, e.g., **easydiffraction** directory (*optional*)
   ```
-  mkdir easyDiffraction && cd easyDiffraction
+  mkdir easydiffraction && cd easydiffraction
   ```
 * Create virtual environment and activate it (*optional*)
   ```
@@ -31,25 +30,25 @@ Currently **easyDiffractionLib** is in **alpha** and has not been released on **
   ```
   pip install --upgrade pip
   ```
-* Install **easyDiffractionLib**
+* Install **easydiffraction** with extras
   ```
-  pip install easyDiffraction --extra-index-url https://easyscience.github.io/pypi
+  pip install 'easydiffraction[charts] @ git+https://github.com/easyscience/easydiffractionlib.git@new_job_dev2'
   ```
 
 ## Examples
 
-### Jupyter Notebook examples that use easyDiffractionLib
+### Jupyter Notebook examples that use EasyDiffraction
 
 #### Locally
 
-* Install **easyDiffractionLib** as described above
-* Install Jupyter Notebook and visualization libraries, such as **py3Dmol** and **bokeh** (*if not done already*)
+* Install **easydiffraction** as described above, including `charts` extras for visualization
+* Install Jupyter Notebook
   ```
-  pip install notebook py3Dmol bokeh
+  pip install notebook
   ```
-* Download **easyDiffractionLib** Jupyter Notebook [examples](https://github.com/easyScience/easyDiffractionLib/tree/master/examples) from GitHub, e.g., using **svn** (*if not done already*)
+* Download **easyDiffractionLib** Jupyter Notebook [examples](https://github.com/easyscience/easydiffractionlib/tree/new_job_dev2/examples) from GitHub, e.g., using **svn** (*if not done already*)
   ```
-  svn export https://github.com/easyScience/easyDiffractionLib/branches/master/examples
+  svn export https://github.com/easyscience/easydiffractionlib/branches/new_job_dev2/examples
   ```
 * Run Jupyter Notebook server
   ```
@@ -61,14 +60,21 @@ Currently **easyDiffractionLib** is in **alpha** and has not been released on **
   ```
 * Select one of the ***.ipynb** files
 
-#### Via Binder (interactive)
+#### Via Google Colab (interactive, requires google account)
+
+##### Neutron powder diffraction
 
-Examples can also be run on the online service [**Binder**](https://mybinder.org/). Click [launch **Binder**](https://mybinder.org/v2/gh/easyScience/easyDiffractionLib/master) and navigate to the examples folder to run one of the notebooks or create your own.
+* [Fitting, constant wavelength, La0.5Ba0.5CoO3 - HRPT@PSI](https://colab.research.google.com/github/EasyScience/EasyDiffractionLib/blob/new_job_dev2/examples/Fitting_PD-NEUT-CW_LBCO-HRPT.ipynb)
+* [Fitting, time-of-flight, Si - SEPD@Argonne](https://colab.research.google.com/github/EasyScience/EasyDiffractionLib/blob/new_job_dev2/examples/Fitting_PD-NEUT-TOF_Si-SEPD.ipynb)
+* [Fitting, time-of-flight, Na2Ca3Al2F14 - WISH@ISIS](https://colab.research.google.com/github/EasyScience/EasyDiffractionLib/blob/new_job_dev2/examples/Fitting_PD-NEUT-TOF_NCAF-WISH.ipynb)
 
 #### Via nbviewer (non-interactive preview)
 
-* [Simulation](https://nbviewer.jupyter.org/github/easyScience/easyDiffractionLib/blob/master/examples/Simulation.ipynb)
-* [Fitting](https://nbviewer.jupyter.org/github/easyScience/easyDiffractionLib/blob/master/examples/Fitting.ipynb)
+##### Neutron powder diffraction
+
+* [Fitting, constant wavelength, La0.5Ba0.5CoO3 - HRPT@PSI](https://nbviewer.org/github/EasyScience/EasyDiffractionLib/blob/new_job_dev2/examples/Fitting_PD-NEUT-CW_LBCO-HRPT.ipynb)
+* [Fitting, time-of-flight, Si - SEPD@Argonne](https://nbviewer.org/github/EasyScience/EasyDiffractionLib/blob/new_job_dev2/examples/Fitting_PD-NEUT-TOF_Si-SEPD.ipynb)
+* [Fitting, time-of-flight, Na2Ca3Al2F14 - WISH@ISIS](https://nbviewer.org/github/EasyScience/EasyDiffractionLib/blob/new_job_dev2/examples/Fitting_PD-NEUT-TOF_NCAF-WISH.ipynb)
 
 ## Test
 

diff --git a/easyDiffractionLib/Interfaces/__init__.py b/easyDiffractionLib/Interfaces/__init__.py
diff --git a/easyDiffractionLib/__init__.py b/easyDiffractionLib/__init__.py
diff --git a/easyDiffractionLib/Interfaces/CFML.py → easydiffraction/Interfaces/CFML.py b/easyDiffractionLib/Interfaces/CFML.py → easydiffraction/Interfaces/CFML.py
@@ -5,18 +5,18 @@
 import os
 
 import numpy as np
-from easyCore import borg
-from easyCore.Objects.Inferface import ItemContainer
+from easyscience import global_object as borg
+from easyscience.Objects.Inferface import ItemContainer
 
-from easyDiffractionLib import Lattice
-from easyDiffractionLib import Phase
-from easyDiffractionLib import Phases
-from easyDiffractionLib import Site
-from easyDiffractionLib import SpaceGroup
-from easyDiffractionLib.calculators.CFML import CFML as CFML_calc
-from easyDiffractionLib.Interfaces.interfaceTemplate import InterfaceTemplate
-from easyDiffractionLib.Profiles.P1D import Instrument1DCWParameters
-from easyDiffractionLib.Profiles.P1D import Powder1DParameters
+from easydiffraction import Lattice
+from easydiffraction import Phase
+from easydiffraction import Phases
+from easydiffraction import Site
+from easydiffraction import SpaceGroup
+from easydiffraction.calculators.CFML import CFML as CFML_calc
+from easydiffraction.Interfaces.interfaceTemplate import InterfaceTemplate
+from easydiffraction.Profiles.P1D import Instrument1DCWParameters
+from easydiffraction.Profiles.P1D import Powder1DParameters
 
 
 class CFML(InterfaceTemplate):
@@ -86,7 +86,7 @@ def feature_checker(
         )
 
     def create(self, model):
-        from easyDiffractionLib.sample import Sample
+        from easydiffraction.sample import Sample
 
         r_list = []
         t_ = type(model)
@@ -131,9 +131,6 @@ def create(self, model):
             self.__createModel(model)
         elif t_.__name__ in ["Powder1DCW", "powder1DCW", "Npowder1DCW", "Npowder1DCWunp"]:
             self.__createModel(model)
-        else:
-            if self._borg.debug:
-                print(f"I'm a: {type(model)}")
         return r_list
 
     def link_atom(self, crystal_obj, atom):
@@ -223,4 +220,4 @@ def get_total_y_for_phases(self) -> list:
 
     @staticmethod
     def __identify(obj):
-        return borg.map.convert_id_to_key(obj)
+        return obj.unique_name
diff --git a/easyDiffractionLib/Interfaces/GSASII.py → easydiffraction/Interfaces/GSASII.py b/easyDiffractionLib/Interfaces/GSASII.py → easydiffraction/Interfaces/GSASII.py
@@ -2,15 +2,15 @@
 __version__ = "0.0.2"
 
 import numpy as np
-from easyCore import borg
-from easyCore.Objects.Inferface import ItemContainer
+from easyscience import global_object as borg
+from easyscience.Objects.Inferface import ItemContainer
 
-from easyDiffractionLib import Lattice
-from easyDiffractionLib import Phases
-from easyDiffractionLib import Site
-from easyDiffractionLib import SpaceGroup
-from easyDiffractionLib.Profiles.P1D import Instrument1DCWParameters
-from easyDiffractionLib.Profiles.P1D import Powder1DParameters
+from easydiffraction import Lattice
+from easydiffraction import Phases
+from easydiffraction import Site
+from easydiffraction import SpaceGroup
+from easydiffraction.Profiles.P1D import Instrument1DCWParameters
+from easydiffraction.Profiles.P1D import Powder1DParameters
 
 from ..calculators.GSASII import GSASII as GSAS_calc
 from ..Interfaces.interfaceTemplate import InterfaceTemplate
@@ -79,7 +79,7 @@ def feature_checker(radiation='N', exp_type='CW', sample_type='powder', dimensio
                                           FEATURES=GSASII.feature_available)
 
     def create(self, model):
-        from easyDiffractionLib.sample import Sample
+        from easydiffraction.sample import Sample
         r_list = []
         t_ = type(model)
         model_key = self.__identify(model)
@@ -121,9 +121,7 @@ def create(self, model):
             self.__createModel(model)
         elif issubclass(t_, Sample):
             self.__createModel(model)
-        else:
-            if self._borg.debug:
-                print(f"I'm a: {type(model)}")
+
         return r_list
 
     def link_atom(self, crystal_obj, atom):

diff --git a/easydiffraction/Interfaces/__init__.py b/easydiffraction/Interfaces/__init__.py
@@ -0,0 +1,28 @@
+__author__ = 'github.com/wardsimon'
+__version__ = '0.0.1'
+
+
+try:
+    from easydiffraction.Interfaces.cryspyV2 import CryspyBase  # noqa: F401
+except ImportError:
+    print('Warning: CrysPy is not installed')
+
+# Temporarily disabling the CrysFML and GSASII interfaces
+# try:
+#     from easydiffraction.Interfaces.CFML import CFML  # noqa: F401
+# except ImportError:
+#     print('Warning: CrysFML is not installed')
+
+# try:
+#     from easydiffraction.Interfaces.GSASII import GSASII  # noqa: F401
+# except ImportError:
+#     print('Warning: GSAS-2 is not installed')
+
+try:
+    from easydiffraction.Interfaces.pdffit2 import Pdffit2  # noqa: F401
+except ImportError:
+    pass
+    #print('Warning: PdfFit2 is not installed')
+
+from easydiffraction.Interfaces.interfaceTemplate import InterfaceTemplate as InterfaceTemplate  # noqa: F401
+