Merge pull request #280 from jmfee-usgs/develop-docs

Develop docs - 

.flake8

-[flake8]
-count = True
-exclude = .git,__pycache,node_modules,.ipynb_checkpoints
-# This project uses PEP8 with the following exceptions:
-# - continuation lines should use 2 levels of indentation (8 spaces)
-#   E122: continuation line missing indentation or outdented
-#   E126: continuation line over-indented for hanging indent
-#   E127: continuation line over-indented for visual indent
-#   E128: continuation line under-indented for visual indent
-#   E131: continuation line unaligned for hanging indent
-# - short variables should be avoided, but not currently enforced
-#   E741: do not use variables named ‘l’, ‘O’, or ‘I’
-# - both W503 and W504 are enabled, but contradictory.
-#   code currently appears to adhere to W503.
-#   W504: line break after binary operator
-ignore = E122, E126, E127, E128, E131, E741, W504

.gitignore

@@ -6,4 +6,7 @@ coverage.xml
 .ipynb_checkpoints*
 .pytest_cache
 htmlcov
-.vscode
\ No newline at end of file
+.vscode
+build
+dist
+*.egg-info
\ No newline at end of file

Dockerfile

-ARG BUILD_IMAGE=usgs/centos:7
-ARG FROM_IMAGE=usgs/centos:7
-FROM $BUILD_IMAGE AS pycurl-build
+ARG FROM_IMAGE=usgs/centos:8
+
+FROM $FROM_IMAGE
+LABEL maintainer="Jeremy Fee <jmfee@usgs.gov>"
 
-# install conda dependencies
-RUN yum install -y \
-        bzip2 \
-        gcc \
-        libcurl-devel \
-    && yum clean all
 
 # install conda
 ENV PATH /conda/bin:$PATH
@@ -21,29 +16,24 @@ RUN echo 'export PATH=/conda/bin:$PATH' > /etc/profile.d/conda.sh \
 # install dependencies via conda
 RUN conda config --set ssl_verify $SSL_CERT_FILE \
     && conda config --add channels conda-forge \
-    && conda install --yes jupyter obspy \
-    # build pycurl with SFTP support
+    && conda install --yes jupyter obspy pycurl \
+    && conda clean --all -y \
     && export PIP_CERT=$SSL_CERT_FILE \
-    && export PYCURL_SSL_LIBRARY=nss \
-    && pip install pycurl \
-    # clean up
-    && conda clean --all -y
-
+    && pip install \
+        authlib \
+        flask \
+        flask-login \
+        flask-migrate \
+        flask-session \
+        flask-sqlalchemy \
+        psycopg2-binary
 
-FROM $FROM_IMAGE
-LABEL maintainer="Jeremy Fee <jmfee@usgs.gov>"
-
-# use conda install from build container
-ENV PATH /conda/bin:$PATH
-COPY --from=pycurl-build /conda /conda
-COPY --from=pycurl-build /etc/profile.d/conda.sh /etc/profile.d/conda.sh
 
 # copy library (ignores set in .dockerignore)
 COPY . /geomag-algorithms
 
 
-RUN pip install /geomag-algorithms \
-    && useradd \
+RUN useradd \
         -c 'Docker image user' \
         -m \
         -r \

Makefile

+
+.PHONY: build clean coverage format test
+
+build:
+	python setup.py bdist_wheel -d dist
+
+clean:
+	# run in interactive mode
+	git clean -i
+
+coverage:
+    pytest --cov=geomagio --cov-report xml
+
+format:
+	black .
+
+test:
+	pytest

Pipfile

@@ -4,7 +4,6 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
-flake8 = "*"
 pytest = "*"
 pytest-cov = "*"
 webtest = "*"

docker-entrypoint.sh

@@ -4,21 +4,21 @@
 # "exec" seems like a much simpler solution for this,
 # however, jupyter kernels die noisy deaths when using exec.
 
-_term () {
-  echo 'Caught SIGERM'
-  kill -TERM "$child"
-}
-trap _term SIGTERM
+# _term () {
+#  echo 'Caught SIGTERM'
+#  kill -TERM "$child"
+#}
+#trap _term SIGTERM
 
 # add geomagio to notebook path
 export PYTHONPATH=/geomag-algorithms
 
 # run jupyter notebook server
-jupyter notebook \
+exec jupyter notebook \
     --ip='*' \
     --notebook-dir=/home/geomag_user/notebooks \
     --no-browser \
-    --port=8000 &
+    --port=8000
 
-child=$!
-wait "$child"
+#child=$!
+#wait "$child"

docs/develop.md

-Development Dependencies
-========================
+# Development Dependencies
 
 These instructions only need to be completed if you plan on developing new
-code for this project, and may also be used to run a local copy of the code.
+code for this project, but may also be used to run a local copy of the code.
 
+## Clone Project
 
-Begin Developing
-----------------
+This project uses a forking workflow.
+https://guides.github.com/activities/forking/
 
-1. Install `obspy`, `pycurl`, `flake8`, `pytest`, `pytest-cov`, `webtest`.
-> Using Anaconda is recommended ( https://conda.io/miniconda.html ).
+1.  Fork this project on Github.
 
-        conda config --add channels conda-forge
-        conda create --name geomagenv obspy pycurl flake8 pytest pytest-cov webtest
-        source activate geomagenv
+    https://github.com/usgs/geomag-algorithms.git
 
-2. Fork this project on Github ( https://guides.github.com/activities/forking/ ).
-
-        https://github.com/{YOUR_GITHUB_ACCOUNT}/geomag-algorithms.git
-
-3. Clone your fork
+2.  Clone your fork
 
         git clone https://github.com/{YOUR_GITHUB_ACCOUNT}/geomag-algorithms.git
         cd geomag-algorithms
         git remote add upstream https://github.com/usgs/geomag-algorithms.git
 
-4. Use branches to develop new features and submit pull requests.
+3.  Use branches to develop new features and submit pull requests.
 
+## Install Dependencies
 
-Developer Tools
----------------
+- Using `pipenv`
+  https://pipenv.kennethreitz.org/en/latest/
 
-- **Linting errors**
-Check for linting errors using Flake8
+  > `pyenv` is also useful for installing specific/multiple versions of python
+  >
+  > - https://github.com/pyenv/pyenv
+  > - https://github.com/pyenv-win/pyenv-win
 
-        cd geomag-algorithms
-        flake8
+      pipenv install --dev
+      pipenv shell
+
+- Or, using Miniconda/Anaconda
+  https://conda.io/miniconda.html
+
+      conda config --add channels conda-forge
+      conda create --name geomagenv obspy pycurl black pre-commit pytest pytest-cov webtest
+      conda activate geomagenv
+
+## Coding Standards
+
+This project uses _The Black Code Style_
+https://black.readthedocs.io/en/stable/the_black_code_style.html
+
+## Developer Tools
+
+- **Code Formatting**
+
+  This project uses the `black` formatter, combined with `pre-commit`, to
+  automatically format code before it is committed.
+
+  VSCode ( https://code.visualstudio.com/ ), with the `Python` extension,
+  can be configured to automatically format using `black` when files are saved.
+  The `Formatting Toggle` extension is also useful.
+
+  You can also manually format all files in the project by running
+
+      black .
 
 - **Unit tests**
-Run unit tests using PyTest
 
-        cd geomag-algorithms
-        pytest
+  Run unit tests using PyTest
 
-- **Unit test coverage**
+      pytest
 
-        cd geomag-algorithms
-        pytest --cov=geomagio
+- **Unit test coverage**
 
-- **Automatically run linting and tests while developing**
-(Requires NodeJS)
+      pytest --cov=geomagio
 
-        cd geomag-algorithms
-        npm install
-        npm run watch
+## Routine Git Updates
 
-    There are also "npm run" aliases for individual commands which are listed by running
+- **Pulling new changes**
 
-        npm run
+  When starting a new branch, or before putting in a pull request, make sure
+  you have the latest changes from the `upstream` repository.
 
+  > The local master branch should only be used for synchonization with the
+  > `upstream` repository, and we recommend always using the `--ff-only` option.
 
-Coding Standards
-----------------
+      git checkout master
+      git pull --ff-only upstream master
 
-This project adheres to PEP8 standards in most cases:
-    https://www.python.org/dev/peps/pep-0008
+- **Rebase an existing branch**
 
-**PEP8 Exceptions**
+  After downloading updates into the master branch, feature branches need to be
+  rebased so they include any already merged changes.
 
-- Hanging/Visual indents (E122, E126, E127, E128, E131)
+      git checkout FEATURE-BRANCH
+      git rebase master
 
-    - line continuations should use two indentations (8 spaces).
-    - do not use visual indents.
+  Resolve any rebase conflicts.
+  If you have already pushed this branch to your fork, you may need to force push
+  because branch history has changed.

setup.py

-from distutils.core import setup
+import setuptools
 
-setup(
+setuptools.setup(
     name="geomag-algorithms",
-    version="1.0.0",
-    description="USGS Geomag IO Library",
+    version="1.0.1",
+    description="USGS Geomag Algorithms Library",
     url="https://github.com/usgs/geomag-algorithms",
-    packages=[
-        "geomagio",
-        "geomagio.algorithm",
-        "geomagio.binlog",
-        "geomagio.edge",
-        "geomagio.iaga2002",
-        "geomagio.imfjson",
-        "geomagio.imfv122",
-        "geomagio.imfv283",
-        "geomagio.pcdcp",
-        "geomagio.temperature",
-        "geomagio.vbf",
-    ],
-    install_requires=["numpy", "matplotlib", "scipy", "obspy", "pycurl"],
+    packages=setuptools.find_packages(exclude=["test*"]),
+    python_requires=">=3.6, <4",
+    install_requires=["obspy"],
+    extras_require={
+        "url": ["pycurl"],
+        "webservice": [
+            "authlib",
+            "flask",
+            "flask-login",
+            "flask-migrate",
+            "flask-session",
+            "flask-sqlalchemy",
+            "psycopg2-binary",
+        ],
+    },
     scripts=["bin/geomag.py", "bin/geomag_webservice.py", "bin/make_cal.py"],
+    project_urls={
+        "Bug Reports": "https://github.com/usgs/geomag-algorithms/issues",
+        "Source": "https://github.com/usgs/geomag-algorithms",
+    },
 )