Merge branch 'develop' into master

.codecov.yml

@@ -0,0 +1,12 @@
+codecov:
+    branch: develop
+
+coverage:
+  status:
+    project:
+      default:
+        target: 1
+    patch: false
+    changes: false
+
+comment: off

.coveragerc

@@ -3,3 +3,4 @@ omit =
     setup.py
     tests/*
     hydrodata/__init__.py
+    hydrodata/print_versions.py

.deepsource.toml

@@ -0,0 +1,19 @@
+version = 1
+
+test_patterns = [
+    "*/tests/**",
+    "*/test_*.py"
+]
+
+exclude_patterns = [
+    "docs/**",
+    "ci/**",
+    "*/print_versions.py",
+]
+
+[[analyzers]]
+name = "python"
+enabled = true
+
+  [analyzers.meta]
+  runtime_version = "3.x.x"

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,39 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+<!-- Please include a self-contained copy-pastable example that generates the issue if possible.
+
+Please be concise with code posted. See guidelines below on how to provide a good bug report:
+
+- Craft Minimal Bug Reports: http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports
+- Minimal Complete Verifiable Examples: https://stackoverflow.com/help/mcve
+
+Bug reports that follow these guidelines are easier to diagnose, and so are often handled much more quickly.
+-->
+
+**What happened**:
+
+**What you expected to happen**:
+
+**Minimal Complete Verifiable Example**:
+
+```python
+# Put your MCVE code here
+```
+
+**Anything else we need to know?**:
+
+**Environment**:
+
+<details><summary>Output of <tt>hydrodata.show_versions()</tt></summary>
+
+<!-- Paste the output here hydrodata.show_versions() here -->
+
+
+</details>

.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,22 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+<!-- Please do a quick search of existing issues to make sure that this has not been asked before. -->
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,7 @@
+<!-- Feel free to remove check-list items aren't relevant to your change -->
+
+ - [ ] Closes #xxxx
+ - [ ] Tests added and passed `make coverage`
+ - [ ] Passes `make lint`
+ - [ ] User visible changes (including notable bug fixes) are documented in `HISTORY.rst`
+ - [ ] After adding new functions/methods ran `make apidocs`

.github/workflows/lint.yml

@@ -4,22 +4,14 @@ on: [push, pull_request]
 
 jobs:
   run-linters:
-    name: Run linters
+    name: Run pre-commit
     runs-on: ubuntu-latest
 
     steps:
-      - name: Check out Git repository
-        uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@master
+      - uses: actions/setup-python@master
         with:
           python-version: 3.8
 
-      - name: Install Python dependencies
-        run: pip install -r ci/requirements/requirements_lint.txt
+      - uses: pre-commit/action@v2.0.0
 
-      - run: isort --recursive --diff hydrodata tests
-      - run: black --py36 --diff hydrodata tests
-      - run: pyupgrade --py36-plus
-      - run: flake8 hydrodata tests

.github/workflows/python-publish.yml

@@ -1,4 +1,4 @@
-name: Upload Python Package
+name: pypi publish
 
 on:
   release:
@@ -10,11 +10,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@master
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@master
       with:
-        python-version: '3.8'
+        python-version: 3.8
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/test.yml

@@ -1,38 +1,38 @@
-name: build
+name: pytest
 
 on: [push, pull_request]
 
 jobs:
   test:
-    name: pytest (${{ matrix.python-version }}, ${{ matrix.os }})
+    name: python ${{ matrix.python-version }}, ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         python-version: ["3.6", "3.7", "3.8"]
         os: ["ubuntu-latest", "macos-latest"]
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.5.0
+      - uses: actions/checkout@master
+      - name: Setup miniconda
+        uses: goanpeca/setup-miniconda@v1
         with:
           activate-environment: hydrodata
           python-version: ${{ matrix.python-version }}
           environment-file: ci/requirements/py${{ matrix.python-version }}.yml
           auto-update-conda: true
           auto-activate-base: false
 
-      - name: Install Hydrodata
+      - name: Install hydrodata
         shell: bash -l {0}
         run: |
           conda info
           conda list
-          conda install -y -c conda-forge pytest pytest-runner pytest-cov pytest-xdist codecov
+          conda install -y -c conda-forge pytest pytest-cov codecov flaky
           pip install --no-deps -e .
 
-      - name: Run tests
+      - name: Run pytest
         shell: bash -l {0}
         run: pytest --cov=hydrodata --cov-report term-missing --cov-report xml --verbose --color=yes
 
       - name: Run codecov
-        uses: codecov/codecov-action@v1.0.7
+        uses: codecov/codecov-action@v1

.gitignore

@@ -107,4 +107,4 @@ ENV/
 # logs
 .nvimlog
 data/
-tags
+tags*

.pre-commit-config.yaml

@@ -1,28 +1,58 @@
-# https://pre-commit.com/
 repos:
   # isort should run before black as black sometimes tweaks the isort output
   - repo: https://github.com/timothycrosley/isort
-    rev: 4.3.21-2
+    rev: 5.3.2
     hooks:
       - id: isort
-  # https://github.com/python/black#version-control-integration
+        name: Sort imports with isort
+
   - repo: https://github.com/python/black
-    rev: stable
+    rev: 19.10b0
     hooks:
       - id: black
+        name: Autoformat with black
+        args: [-t, py38, -l, "100"]
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.2.3
+    rev: v3.2.0
+    hooks:
+    - id: trailing-whitespace
+    - id: check-executables-have-shebangs
+    - id: requirements-txt-fixer
+
+  - repo: https://github.com/PyCQA/doc8
+    rev: 0.8.1rc3
+    hooks:
+    - id: doc8
+      name: Autoformat with doc8
+      args: [--max-line-length, "100"]
+
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.3
     hooks:
       - id: flake8
+        name: Linting with flake8
+        exclude: docs/conf.py
+        additional_dependencies: [flake8-comprehensions, flake8-builtins, flake8-blind-except, flake8-bugbear, flake8-use-fstring, flake8-docstrings]
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.761  # Must match ci/requirements/*.yml
+    rev: v0.782
     hooks:
       - id: mypy
+        name: Static type checking with mypy
         files: hydrodata
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v1.22.1
+    rev: v2.7.2
     hooks:
       - id: pyupgrade
-        args:
-          - "--py36-plus"
+        name: Upgrade synax to python 3.6+ with pyupgrade
+        args: [--py36-plus]
+
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.6.2
+    hooks:
+      - id: bandit
+        name: Check for security issues with bandit
+        args: [-lll, --recursive, hydrodata]
+        files: .py$

.readthedocs.yml

@@ -5,3 +5,9 @@ build:
 
 conda:
     environment: ci/requirements/doc.yml
+
+python:
+  install:
+    - method: pip
+      path: .
+

CODE_OF_CONDUCT.rst

@@ -0,0 +1,87 @@
+Contributor Covenant 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, sex
+characteristics, gender identity and expression, level of experience,
+education, socio-economic status, nationality, personal appearance,
+race, religion, or sexual identity and orientation.
+
+Our Standards
+-------------
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+-  Using welcoming and inclusive language
+-  Being respectful of differing viewpoints and experiences
+-  Gracefully accepting constructive criticism
+-  Focusing on what is best for the community
+-  Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+-  The use of sexualized language or imagery and unwelcome sexual
+   attention or advances
+-  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 tchegini@uh.edu. 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 <https://www.contributor-covenant.org>`__, version 1.4,
+available at
+https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq