Merge pull request #10 from harmsm/main

modernized build environment, unit testing

.github/workflows/python-app.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and flake8 across
 # platforms and python versions. 
 
-name: ElliptiCBn
+name: ellipticbn
 
 on:
   push:
@@ -14,21 +14,20 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
-      max-parallel: 3
       matrix:
         os: [ubuntu-latest,macos-latest,windows-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10' , '3.11', '3.12']
+        python-version: ['3.9', '3.10' , '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: install ElliptiCBn
+    - name: install ellipticbn
       run: |
         # platform specific packages
-        python -m pip install . -vv -r requirements.txt
+        python -m pip install . pyproject.toml
 
     - name: run flake8
       run: |

MANIFEST.in

@@ -1,5 +1,3 @@
-include requirements.txt
-include ElliptiCBn/data/
-include ElliptiCBn/data/*.csv
-include ElliptiCBn/data/*.txt
-include notebooks/*.ipynb
+include src/ellipticbn/data/
+include src/ellipticbn/data/*.csv
+include src/ellipticbn/data/*.txt

README.md

@@ -8,7 +8,7 @@
 
 Run the program in the cloud without installing any software. 
 
-<a href="https://githubtocolab.com/harmslab/ElliptiCBn/blob/main/notebooks/ElliptiCBn.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>
+<a href="https://githubtocolab.com/harmslab/ellipticbn/blob/main/notebooks/ellipticbn.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>
 
 
 
@@ -83,25 +83,25 @@ ElliptiCB[n] can be installed locally and used as a command line tool.
 On a terminal, run:
 
 ```bash
-pip install ElliptiCBn
+pip install ellipticbn
 ```
 
 **To install from source:**
 
 On a terminal, run:
 
 ```bash
-git clone https://github.com/harmslab/ElliptiCBn.git
-cd ElliptiCBn
-python -m pip install . -vv -r requirements.txt
+git clone https://github.com/harmslab/ellipticbn.git
+cd ellipticbn
+python -m pip install . pyproject.toml
 ```
 
 ### Run from the command line
 
 ElliptiCB[n] takes one or more .xyz files as inputs. Assuming that HUMAR.xyz is in the working directory, running this command:
 
 ```
-$> ElliptiCBn HUMXAR.xyz
+$> ellipticbn HUMXAR.xyz
 ```
 
 Would generate the following output:
@@ -126,7 +126,7 @@ It will also generate HUXMAR.xyz.html (the visualization) and HUXMAR.xyz.xlsx (t
 You can also run the program on multiple xyz files:
 
 ```
-$> ElliptiCBn HUMXAR.xyz LAZPIM.xyz
+$> ellipticbn HUMXAR.xyz LAZPIM.xyz
 ```
 
 Would generate the following output:
@@ -169,13 +169,13 @@ In addition to the visualization html and individual ellipiticty files, this cal
 One can also change the parameters used in the calculation. To see the available options, type the following in a terminal:
 
 ```bash
-ElliptiCBn --help
+ellipticbn --help
 ```
 
 As of this writing (version 2.0.1), this gives the following output:
 
 ```
-usage: ElliptiCBn [-h] [--min_num_carbons MIN_NUM_CARBONS]
+usage: ellipticbn [-h] [--min_num_carbons MIN_NUM_CARBONS]
                   [--max_num_carbons MAX_NUM_CARBONS]
                   [--guest_search_radius GUEST_SEARCH_RADIUS]
                   [--summary_file SUMMARY_FILE] [--output_dir OUTPUT_DIR]

notebooks/ElliptiCBn.ipynb → notebooks/ellipticbn.ipynb

@@ -8,7 +8,7 @@
         "tags": []
       },
       "source": [
-        "# Use ElliptiCBn to measure the ellipticity of cucurbituril hosts\n",
+        "# Use ellipticbn to measure the ellipticity of cucurbituril hosts\n",
         "\n",
         "\n",
         "### Description\n",
@@ -21,7 +21,7 @@
         "\n",
         "\n",
         "\n",
-        "#### ElliptiCBn performs the following steps\n",
+        "#### ellipticbn performs the following steps\n",
         "\n",
         "<img src=\"https://github.com/harmsm/ElliptiC/raw/main/images/pipeline_image.png\" width=\"600px\"/>\n",
         "\n",
@@ -58,7 +58,7 @@
       "source": [
         "#@title Set up environment\n",
         "\n",
-        "#@markdown This cell configures the computing environment to run ElliptiCBn. Run\n",
+        "#@markdown This cell configures the computing environment to run ellipticbn. Run\n",
         "#@markdown this cell before uploading an XYZ file.\n",
         "\n",
         "#@markdown To run the cell, click the \"Play\" button to the left.\n",
@@ -73,14 +73,14 @@
         "    raise Exception(err) from e\n",
         "\n",
         "if RUNNING_IN_COLAB:\n",
-        "    !git clone https://github.com/harmslab/ElliptiCBn\n",
-        "    %cd ElliptiCBn\n",
-        "    %pip install . -r requirements.txt\n",
+        "    !git clone https://github.com/harmslab/ellipticbn\n",
+        "    %cd ellipticbn\n",
+        "    %pip install . pyproject.toml \n",
         "\n",
         "# ------------------------------------------------------------------------------\n",
         "# Imports\n",
         "\n",
-        "import ElliptiCBn as ec\n",
+        "import ellipticbn as ec\n",
         "\n",
         "import numpy as np\n",
         "import pandas as pd\n",

pyproject.toml

@@ -0,0 +1,61 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[tool.distutils.bdist_wheel]
+universal = true
+
+[tool.setuptools.dynamic]
+version = {attr = "ellipticbn.__version__.__version__"}
+
+[tool.setuptools.package-data]
+"*" = [
+  "src/ellipticbn/data/*.txt",
+  "src/ellipticbn/data/*.csv"
+]
+
+[project]
+name = "ellipticbn"
+dynamic = ["version"]
+dependencies = [
+  "numpy>=1.10",
+  "networkx",
+  "scikit-learn",
+  "plotly",
+  "pandas",
+  "matplotlib",
+  "xlsxwriter",
+  "mdanalysis",
+  "scipy"
+]
+
+requires-python = ">=3.9"
+authors = [
+  {name = "Michael Shavlik", email = "[email protected]"},
+  {name = "Mike Harms", email = "[email protected]"},
+]
+maintainers = [
+  {name = "Mike Harms", email = "[email protected]"}
+]
+description = "Automatically measure the ellipticity of cucurbituril macrocycles!"
+readme = "README.md"
+license = {file = "LICENSE"}
+keywords = ["macrocycle", "cucurbituril", "ellipticity", "chemistry", "geometry", "host", "guest"]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Programming Language :: Python"
+]
+
+[project.urls]
+Repository = "https://github.com/harmslab/ellipticbn.git"
+"Bug Tracker" = "https://github.com/harmslab/ellipticbn/issues"
+
+[project.scripts]
+ellipticbn = "ellipticbn.run_all:main_cli"
+
+[project.optional-dependencies]
+test = [
+  "coverage",
+  "flake8",
+  "pytest"
+ ]

run_all_tests.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 echo "Running flake8"
-flake_test=`flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics`
+flake_test=`flake8 src/ --count --select=E9,F63,F7,F82 --show-source --statistics`
 if [[ "${flake_test}" != 0 ]]; then
     echo "flake failed"
     exit

src/ellipticbn/__version__.py

@@ -0,0 +1,3 @@
+VERSION = (2, 1, 2)
+
+__version__ = '.'.join(map(str, VERSION))