Improve tooling for maintenance (#79)

* Fix for issue with new pandas version  (#77)

* new version of pandas has new option which contains max_rows, need to specify full option path to make sure no ambivalence is possible

* Version to 0.10.2-alpha

Co-authored-by: Ashley Smith <ashley.smith@magneticearth.org>

* Move source file locations

* Move to flit build system

* Fix docs build

* Configure linting with pre-commit

* Apply linting

* Configure linting & tests in GitHub Actions

Co-authored-by: Daniel Santillan <daniel.santillan@eox.at>

.flake8

@@ -0,0 +1,7 @@
+[flake8]
+extend-ignore = E203, E501, E722, B950, T001
+select = C,E,F,W,T,B,B9,I
+per-file-ignores =
+    tests/*: T
+    noxfile.py: T
+    __init__.py:F401

.github/workflows/CI.yml

@@ -1,25 +1,41 @@
 name: CI
 
+
 on:
-  push:
-    branches: [ staging ]
+  workflow_dispatch:
   pull_request:
+  push:
     branches: [ staging ]
-  workflow_dispatch:
 
 jobs:
-  run-tests:
-    runs-on: ${{ matrix.operating-system }}
+  pre-commit:
+    name: Format
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - uses: actions/setup-python@v2
+    - uses: pre-commit/action@v2.0.3
+      with:
+        extra_args: --hook-stage manual --all-files
+
+  checks:
+    name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
     strategy:
+      fail-fast: false
       matrix:
-        operating-system:
-          - ubuntu-latest
-          - windows-latest
-          - macOS-latest
+        python-version: ["3.6", "3.10"]
+        runs-on: [ubuntu-latest, macos-latest, windows-latest]
     steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - name: Setup Nox
-        uses: excitedleigh/setup-nox@v2.0.0
-      - name: Run Nox
-        run: nox
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package
+      run: python -m pip install .[test]
+    - name: Configure token access
+      run: |
+        viresclient set_token "https://vires.services/ows" ${{ secrets.VIRES_TOKEN_SWARM }}
+        viresclient set_default_server https://vires.services/ows
+    - name: Test package
+      run: python -m pytest -ra

.gitignore

@@ -34,4 +34,4 @@ MANIFEST
 docs/_build/
 
 # nox
-.nox
+.nox

.pre-commit-config.yaml

@@ -0,0 +1,94 @@
+repos:
+- repo: https://github.com/psf/black
+  rev: 22.3.0
+  hooks:
+  - id: black-jupyter
+
+- repo: https://github.com/kynan/nbstripout
+  rev: "0.5.0"
+  hooks:
+    - id: nbstripout
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.1.0
+  hooks:
+  - id: check-added-large-files
+  - id: check-case-conflict
+  - id: check-merge-conflict
+  - id: check-symlinks
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: mixed-line-ending
+  - id: requirements-txt-fixer
+  - id: trailing-whitespace
+
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: v1.9.0
+  hooks:
+  - id: python-check-blanket-noqa
+  # - id: python-check-blanket-type-ignore
+  - id: python-no-eval
+  - id: python-use-type-annotations
+  - id: rst-backticks
+  - id: rst-directive-colons
+  - id: rst-inline-touching-normal
+
+- repo: https://github.com/PyCQA/isort
+  rev: 5.10.1
+  hooks:
+  - id: isort
+    # args: ["-a", "from __future__ import annotations"]  # Python 3.7+
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v2.31.1
+  hooks:
+  - id: pyupgrade
+    args: ["--py37-plus"]
+
+# - repo: https://github.com/hadialqattan/pycln
+#   rev: v1.1.0
+#   hooks:
+#   - id: pycln
+#     args: [--config=pyproject.toml]
+
+- repo: https://github.com/asottile/yesqa
+  rev: v1.3.0
+  hooks:
+  - id: yesqa
+    exclude: docs/conf.py
+    additional_dependencies: &flake8_dependencies
+      - flake8-bugbear
+      - flake8-print
+
+- repo: https://github.com/pycqa/flake8
+  rev: 4.0.1
+  hooks:
+  - id: flake8
+    exclude: docs/conf.py
+    additional_dependencies: *flake8_dependencies
+
+# - repo: https://github.com/pre-commit/mirrors-mypy
+#   rev: v0.930
+#   hooks:
+#   - id: mypy
+#     files: src
+#     args: [--show-error-codes]
+
+# - repo: https://github.com/codespell-project/codespell
+#   rev: v2.1.0
+#   hooks:
+#   - id: codespell
+
+- repo: https://github.com/shellcheck-py/shellcheck-py
+  rev: v0.8.0.4
+  hooks:
+  - id: shellcheck
+
+- repo: local
+  hooks:
+  - id: disallow-caps
+    name: Disallow improper capitalization
+    language: pygrep
+    entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+    exclude: .pre-commit-config.yaml

.readthedocs.yml

@@ -0,0 +1,21 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Include PDF and ePub
+formats: all
+
+python:
+  version: 3.8
+  install:
+  - method: pip
+    path: .
+    extra_requirements:
+    - docs

README.rst

@@ -101,6 +101,6 @@ You can reference *viresclient* directly using the DOI of our zenodo_ record. Vi
 
 .. _zenodo: https://doi.org/10.5281/zenodo.2554162
 
-    | "We use the Python package, viresclient [1], to access [...] from ESA's VirES for Swarm service [2]"  
-    | [1] https://doi.org/10.5281/zenodo.2554162  
+    | "We use the Python package, viresclient [1], to access [...] from ESA's VirES for Swarm service [2]"
+    | [1] https://doi.org/10.5281/zenodo.2554162
     | [2] https://vires.services

docs/access_token.rst

@@ -6,14 +6,14 @@ The tokens are managed via the web user interface.
 
 Assuming you have an existing VirES account and you can access
 the VirES web client (https://vires.services or https://aeolus.services),
-you get to token manager via `Manage access tokens` item in your account menu
+you get to token manager via *Manage access tokens* item in your account menu
 (displaying your username)
 
 .. image:: images/vires_token_manager_menu.png
    :align: center
 
 The token manager user interface allows creation of new tokens by pressing the
-`Create New Access Token` button
+*Create New Access Token* button
 
 .. image:: images/vires_token_manager_create_blank.png
    :align: center
@@ -24,7 +24,7 @@ brief label indicating its purpose
 .. image:: images/vires_token_manager_create_filled.png
    :align: center
 
-Once the `Create New Access Token` button has been pressed, a new token is
+Once the *Create New Access Token* button has been pressed, a new token is
 generated and displayed to the user
 
 .. image:: images/vires_token_manager_new_token.png
@@ -42,4 +42,3 @@ The token manager list the active access tokens and allows their revocation
   *The tokens are secret.* Therefore, do not keep thier copies or share them
   with others.  When a token is needed generate new one. When a token is no
   longer needed revoke it.
-

docs/available_parameters.rst

@@ -73,7 +73,7 @@ SW_OPER_MITx_LP_2F     MIT_LP           Minima of the Midlatitude Ionospheric Tr
 SW_OPER_MITx_LP_2F:ID  MIT_LP:ID        -> Boundaries of the MIT - derived from the LP
 SW_OPER_MITxTEC_2F     MIT_TEC          Minima of the MIT - derived from Total Electron Content (TEC)
 SW_OPER_MITxTEC_2F:ID  MIT_TEC:ID       -> Boundaries of the MIT - derived from TEC
-SW_OPER_PPIxFAC_2F     PPI_FAC          Midnight Plasmapause Index (PPI) 
+SW_OPER_PPIxFAC_2F     PPI_FAC          Midnight Plasmapause Index (PPI)
 SW_OPER_PPIxFAC_2F:ID  PPI_FAC:ID       -> Boundaries of the Small-Scale Field Aligned Currents (SSFAC)
 ====================== ================ ===================================================================================================
 
@@ -125,7 +125,7 @@ The ``measurements``, ``models``, and ``auxiliaries`` chosen will match the cade
 ----
 
 ``measurements``
----------------- 
+----------------
 
 Choose combinations of measurements from one of the following sets, corresponding to the collection chosen above. The collection full name or collection type can be given to :py:meth:`viresclient.SwarmRequest.available_measurements` to retrieve the list of available measurements for a given collection (e.g. ``request.available_measurements("SW_OPER_MAGA_LR_1B")``)
 
@@ -184,7 +184,7 @@ AUX_OBSH contains a special variable, ``ObsIndex``, which is set to 0, 1, 2 ...
 
 VOBS products:
 
-==================================== =========================================== 
+==================================== ===========================================
 Collection full name                 Available measurement names
 ==================================== ===========================================
 SW_OPER_VOBS_1M_2\_                  ``SiteCode,B_CF,B_OB,sigma_CF,sigma_OB``
@@ -205,7 +205,7 @@ Models are evaluated along the satellite track at the positions of the time seri
   For a good estimate of the ionospheric field measured by a Swarm satellite (with the core, crust and magnetosphere effects removed) use a composed model defined as:
   ``models=["'CHAOS-full' = 'CHAOS-Core' + 'CHAOS-Static' + 'CHAOS-MMA-Primary' + 'CHAOS-MMA-Secondary'"]``
   `(click for more info) <https://github.com/klaundal/notebooks/blob/master/get_external_field.ipynb>`_
-  
+
   This composed model can also be accessed by an alias: ``models=["CHAOS"]`` which represents the full CHAOS model
 
   See `Magnetic Earth <https://magneticearth.org/pages/models.html>`_ for an introduction to geomagnetic models.
@@ -292,8 +292,7 @@ NB: When using model names containing a hyphen (``-``) then extra single (``'``)
 .. note::
 
   Check other packages such as `hapiclient`_ and others from `PyHC`_ for data from other sources.
-  
+
 .. _`hapiclient`: https://github.com/hapi-server/client-python
 
 .. _`PyHC`: http://heliopython.org/projects/
-

docs/available_parameters_aeolus.rst

@@ -2,4 +2,4 @@ Available parameters for Aeolus
 ===============================
 
 .. note::
-  Details to follow. See https://notebooks.aeolus.services for examples.
+  Details to follow. See https://notebooks.aeolus.services for examples.

docs/cli.rst

@@ -143,7 +143,7 @@ Setting extra constant parameters::
       Timestamp
 
 Removing constant parameters::
- 
+
   $ viresclient clear_upload_parameters https://staging.vires.services/ows
   eff3bd47-0098-45d3-ba9e-158bea0fae12: parameters removed