Enhancement (#2)

* dev refactor

* fix test

* fix tests

* remove unused code

* refactor repo name

* Reviewed @zhu0619's changes. Switched to jinja2 for HTML  broadcaster

* Fixed bug in LoggerBroadcaster

* Fixed release CICD

* Fix CICD

---------

Co-authored-by: cwognum <[email protected]>

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -7,10 +7,10 @@ body:
       value: |
         Please provide the following information.
   - type: input
-    id: alchemy-version
+    id: auroris-version
     attributes:
-      label: Alchemy version
-      description: Value of ``alchemy.__version__``
+      label: Auroris version
+      description: Value of ``auroris.__version__``
       placeholder: 0.2.5, 0.3.0, 0.3.1, etc.
     validations:
       required: true
@@ -34,7 +34,7 @@ body:
     id: installation
     attributes:
       label: Installation
-      description: How was Alchemy installed?
+      description: How was Auroris installed?
       placeholder: e.g., "using pip into virtual environment", or "using conda"
     validations:
       required: true
@@ -56,4 +56,4 @@ body:
     id: additional-output
     attributes:
       label: Additional output
-      description: If you think it might be relevant, please provide the output from ``pip freeze`` or ``conda env export`` depending on which was used to install Alchemy.
+      description: If you think it might be relevant, please provide the output from ``pip freeze`` or ``conda env export`` depending on which was used to install Auroris.

.github/workflows/doc.yml

@@ -31,7 +31,11 @@ jobs:
           cache-downloads: true
 
       - name: Install library
-        run: python -m pip install --no-deps .
+        run: |
+          python -m pip install --no-deps .
+          # Note: Temporarily upgrade mkdocs-jupyter through PyPi
+          # See https://github.com/conda-forge/mkdocs-jupyter-feedstock/pull/30
+          python -m pip install mkdocs-jupyter -U --force-reinstall
 
       - name: Configure git
         run: |

.github/workflows/release.yml

@@ -100,7 +100,11 @@ jobs:
           git push origin "${{ inputs.release-version }}"
 
       - name: Install library
-        run: python -m pip install --no-deps .
+        run: |
+          python -m pip install --no-deps .
+          # Note: Temporarily upgrade mkdocs-jupyter through PyPi
+          # See https://github.com/conda-forge/mkdocs-jupyter-feedstock/pull/29
+          python -m pip install mkdocs-jupyter -U --force-reinstall
 
       - name: Build the wheel and sdist
         run: python -m build --no-isolation

.github/workflows/test.yml

@@ -43,7 +43,12 @@ jobs:
             python=${{ matrix.python-version }}
 
       - name: Install library
-        run: python -m pip install --no-deps -e . # -e (editable is needed for code coverage)
+        run: |
+          python -m pip install --no-deps .
+          # Note: Temporarily upgrade mkdocs-jupyter through PyPi
+          # See https://github.com/conda-forge/mkdocs-jupyter-feedstock/pull/30
+          python -m pip install mkdocs-jupyter -U --force-reinstall
+
 
       - name: Install UMAP
         run: python -m pip install umap-learn  # Optional dependency
@@ -52,7 +57,7 @@ jobs:
         run: pytest
 
       - name: Test CLI
-        run: alchemy --help
+        run: auroris --help
 
       - name: Test building the doc
         run: mkdocs build

README.md

@@ -1,13 +1,13 @@
-# Alchemy
+# Auroris
 
 Tools for data curation in the Polaris ecosystem. 
 
 
 ### Getting started
 
 ```python
-from alchemy.curation import Curator
-from alchemy.curation.actions import MoleculeCuration, OutlierDetection, Discretization
+from auroris.curation import Curator
+from auroris.curation.actions import MoleculeCuration, OutlierDetection, Discretization
 
 # Define the curation workflow
 curator = Curator(