Merge pull request #1 from eagles-project/new_branch

New project and package structure sprint

.github/workflows/run_esmac_diags_tests.yml

@@ -0,0 +1,25 @@
+name: run_esmac_diags_ci.yml
+on: [push,pull_request ]
+jobs:
+  build_and_publish:
+    name: Setup Environment, and run test suite
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup Environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: 3.7
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+          activate-environment: esmac_diags
+          environment-file: environment.yml
+      - name: Install esmac_diags
+        shell: bash -l {0}
+        run: |
+          pip install -e .
+      - name: Run Pytest
+        shell: bash -l {0}
+        run: |
+          pytest

.gitignore

@@ -0,0 +1,138 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

README.md

@@ -3,23 +3,28 @@
 
 This Earth System Model (ESM) aerosol-cloud diagnostics package (ESMAC Diags) is currently used to evaluate aerosols, clouds and aerosol-cloud interactions simulated by the Department of Energy’s (DOE) Energy Exascale Earth System Model (E3SM). The first version (v1.0) focuses on comparing simulated aerosol properties with in-situ aircraft, ship and surface measurements. Various types of diagnostics and metrics are performed for aerosol number, size distribution, chemical composition, and CCN concentration to assess how well E3SM represents observed aerosol properties across spatial scales. Metrics for various meteorological and aerosol precursor quantities from the same field campaigns are also included. Version 2 is under development focusing on aerosol-cloud interactions.
 
-More information can be found in README_ESMAC_Diags_v1.0.pdf
+More information can be found in README_ESMAC_Diags_v1.0-alpha.pdf
 
-# Package dependencies
-This code is dependent on the following python packages:
+## To install
+This code is best run using a conda virtual environment. To install the required environment one can do
+```bash
+conda env create -f environment.yml
+```
+to set up a esmac_diags environment. Note if running this on a HPC system, you may need to load the appropriate module for anaconda. 
 
-os
-sys
-glob
-time
-numpy
-scipy
-matplotlib
-netCDF4
+Once the environment has been created you can activate it with ```conda activate esmac_diags``` and then this code can be installed with
+```bash
+pip install -e .
+```
+Which will install the code as editable allowing you to make changes to the codebase and it be reflected in the installed package. 
 
 
 # Test run
-To verify the package, enter scripts/ directory and run scripts_testcase.csh. Then check the directory in testcase/figures/. There should be three figures generated:
+To verify the package, enter scripts/ directory and run 
+```bash
+python run_testcase.py
+```
+Then go to the directory in testcase/figures/. There should be three figures generated:
 
 flighttrack_ACEENA_20170630a.png
 

environment.yml

@@ -0,0 +1,17 @@
+name: esmac_diags
+channels:
+  - conda-forge
+  - anaconda
+  - defaults
+dependencies:
+  - pip
+  - matplotlib
+  - numpy
+  - scipy
+  - sphinx
+  - conda-build
+  - pytest
+  - pytest-shutil
+  - ipython
+  - black
+  - netCDF4

pyproject.toml

@@ -0,0 +1,11 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "-ra -q"
+testpaths = [
+    "tests"
+]
+norecursedirs = "src/esmac_diags/*"