package update and test fixes

.gitignore

@@ -217,7 +217,7 @@ examples/**/*.csv
 # This is incase you run the figure tests
 figure_test_images*
 tags
-sunkit_instruments/version.py
+sunkit_instruments/_version.py
 
 ### Pycharm(?)
 .idea

.pre-commit-config.yaml

@@ -60,7 +60,7 @@ repos:
   # W605 - Fix invalid escape sequence 'x'.
   # W690 - Fix various deprecated code (via lib2to3).
   - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.3
+    rev: 3.8.4
     hooks:
       - id: flake8
         args: ['--count', '--select', 'E101,E11,E111,E112,E113,E121,E122,E123,E124,E125,E126,E127,E128,E129,E131,E133,E20,E211,E231,E241,E242,E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306,E401,E402,E502,E701,E711,E712,E713,E714,E722,E731,E901,E902,F822,F823,W191,W291,W292,W293,W391,W601,W602,W603,W604,W605,W690']
@@ -72,13 +72,13 @@ repos:
         args: ['--in-place', '--remove-all-unused-imports', '--remove-unused-variable']
         exclude: ".*(.fits|.fts|.fit|.txt|tca.*|extern.*|.rst|.md|docs/conf.py)$"
   - repo: https://github.com/timothycrosley/isort
-    rev: 5.5.2
+    rev: 5.6.4
     hooks:
       - id: isort
         args: ['--sp','setup.cfg']
         exclude: ".*(.fits|.fts|.fit|.txt|tca.*|extern.*|.rst|.md|docs/conf.py)$"
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v3.3.0
     hooks:
       - id: check-ast
       - id: check-case-conflict

MANIFEST.in

@@ -15,3 +15,7 @@ prune docs/_build
 prune docs/api
 
 global-exclude *.pyc *.o
+
+# This subpackage is only used in development checkouts and should not be
+# included in built tarballs
+prune sunkit_instruments/_dev

azure-pipelines.yml

@@ -30,53 +30,98 @@ trigger:
     - '*pre*'
     - '*post*'
 
-jobs:
-- template: run-tox-env.yml@OpenAstronomy
-  parameters:
-    submodules: false
-    coverage: codecov
-    toxdeps: tox-pypi-filter
-    posargs: -n=4
-    libraries:
-      apt:
-        - graphviz
-
-    envs:
-      - macos: py38
-        name: py38_test
-
-      - windows: py37
-        name: py37_test
-
-      - linux: py38-online
-        name: py38_test_online
-        posargs: -n=1
-
-      - linux: codestyle
-        name: python_codestyle
-        pytest: false
-
-      - linux: py37-oldestdeps
-        name: py37_test_oldestdeps
-
-      - linux: py38-devdeps
-
-# On branches which aren't master, and not Pull Requests, build the wheels but only upload them on tags
-- ${{ if and(ne(variables['Build.Reason'], 'PullRequest'), not(contains(variables['Build.SourceBranch'], 'master'))) }}:
-  - template: publish.yml@OpenAstronomy
-    parameters:
-      # Only Upload to PyPI on tags
-      ${{ if startsWith(variables['Build.SourceBranch'], 'refs/tags/') }}:
-        pypi_connection_name : 'PyPI'
-      test_extras: 'dev'
-      test_command: 'pytest -p no:warnings --doctest-rst -m "not figure" --pyargs sunkit_instruments'
-      submodules: false
-
-      targets:
-        - wheels_universal
-        - sdist
-      dependsOn:
-        - py37_test
-        - py38_test
-        - py38_test_online
-        - py37_test_oldestdeps
+pr:
+  autoCancel: true
+
+stages:
+  - stage: FirstPhaseTests
+    displayName: Core Tests
+    jobs:
+    - template: run-tox-env.yml@OpenAstronomy
+      parameters:
+        default_python: '3.8'
+        submodules: false
+        coverage: codecov
+        toxdeps: tox-pypi-filter
+        posargs: -n=4
+
+        envs:
+          - linux: codestyle
+            name: style_check
+            pytest: false
+            libraries: {}
+
+          - linux: py38
+
+  - stage: SecondPhaseTests
+    displayName: Stage 2 Tests
+    dependsOn: FirstPhaseTests
+    jobs:
+    - template: run-tox-env.yml@OpenAstronomy
+      parameters:
+        default_python: '3.8'
+        submodules: false
+        coverage: codecov
+        toxdeps: tox-pypi-filter
+        posargs: -n=4
+
+        libraries:
+          apt:
+            - graphviz
+
+        envs:
+          - macos: py37
+
+          - windows: py39
+
+          - linux: build_docs
+            posargs: " "
+            pytest: false
+
+          - linux: py38-online
+
+          - linux: py37-oldestdeps
+
+
+  - ${{ if or(eq(variables['Build.Reason'], 'Schedule'), eq(variables['Build.Reason'], 'Manual')) }}:
+    - stage: CronTests
+      displayName: Cron Tests
+      dependsOn: []  # Don't wait on other stages
+      jobs:
+      - template: run-tox-env.yml@OpenAstronomy
+        parameters:
+          default_python: '3.8'
+          submodules: false
+          coverage: codecov
+          toxdeps: tox-pypi-filter
+          posargs: -n=4
+
+          libraries:
+            yum:
+              - openssl-devel
+              - freetype-devel
+              - libpng-devel
+              - hdf5-devel
+
+          envs:
+            - linux32: py38-32bit
+              manylinux_image: manylinux2010_i686
+
+            - linux: py38-devdeps
+
+  # On branches which aren't master, and not Pull Requests, build the wheels but only upload them on tags
+  - ${{ if and(ne(variables['Build.Reason'], 'PullRequest'), or(ne(variables['Build.SourceBranchName'], 'master'), eq(variables['Build.Reason'], 'Schedule'), eq(variables['Build.Reason'], 'Manual'))) }}:
+    - stage: Release
+      dependsOn: SecondPhaseTests
+      jobs:
+      - template: publish.yml@OpenAstronomy
+        parameters:
+          # Only Upload to PyPI on tags
+          ${{ if startsWith(variables['Build.SourceBranch'], 'refs/tags/') }}:
+            pypi_connection_name : 'PyPI'
+          test_extras: 'dev'
+          test_command: 'pytest -p no:warnings --doctest-rst --pyargs sunkit_instruments'
+          submodules: false
+          targets:
+            - wheels_universal
+            - sdist

docs/code_ref/goes_xrs.rst

@@ -1 +1 @@
-.. automodapi:: sunkit_instruments.fermi
+.. automodapi:: sunkit_instruments.goes_xrs

pyproject.toml

@@ -25,10 +25,6 @@ build-backend = 'setuptools.build_meta'
 
     number_incorrect_long = "The number in the changelog file you added does not match the number of this pull request. Please rename the file."
 
-  [ tool.gilesbot.milestones ]
-    enabled = true
-    missing_message_long = "This pull request does not have a milestone assigned to it. Only maintainers can change this, so you don't need to worry about it. :smile:"
-
 [tool.towncrier]
     package = "sunkit_instruments"
     filename = "CHANGELOG.rst"

setup.cfg

@@ -12,7 +12,7 @@ url = https://sunpy.org
 edit_on_github = True
 github_project = sunpy/sunkit_instruments
 platform = any
-keywords = solar physics, solar, science, sun, wcs, coordinates
+keywords = solar physics, solar, science, telescope, instrumentation
 classifiers =
   Intended Audience :: Science/Research
   License :: OSI Approved :: BSD License
@@ -32,11 +32,11 @@ include_package_data = True
 setup_requires =
   setuptools_scm
 install_requires =
+  astropy
+  matplotlib
   numpy
   pandas
-  sunpy[net] >= 2.0.0
-  matplotlib
-  astropy
+  sunpy[net,timeseries] >= 2.0.0
 
 [options.extras_require]
 tests =
@@ -47,22 +47,22 @@ tests =
 docs =
   sphinx
   sphinx-automodapi
-  towncrier
   sunpy-sphinx-theme
+  towncrier
+
+[options.packages.find]
+exclude = sunkit_instruments._dev
 
 [tool:pytest]
-minversion = 3.0
 testpaths = "sunkit_instruments" "docs"
-norecursedirs = ".tox" "build" "docs[\/]_build" "docs[\/]generated" "*.egg-info" "examples" ".jupyter" ".history" "tools"
+norecursedirs = ".tox" "build" "docs[\/]_build" "docs[\/]generated" "*.egg-info" "examples" ".history" "sunkit_instruments/_dev"
 doctest_plus = enabled
 doctest_optionflags = NORMALIZE_WHITESPACE FLOAT_CMP ELLIPSIS
 addopts = -rsa -vvv --doctest-rst --doctest-ignore-import-errors
 markers =
     remote_data: marks this test function as needing remote data.
     online: marks this test function as needing online connectivity.
-    figure: marks this test function as using hash-based Matplotlib figure verification. This mark is not meant to be directly applied, but is instead automatically applied when a test function uses the @sunpy.tests.helpers.figure_test decorator.
-    flaky
-    array_compare
+    array_compare: compare arrays
 remote_data_strict = True
 # Pin junit behaviour; we might want to update this to xunit2 at some point
 junit_family=xunit1
@@ -116,24 +116,24 @@ sections = STDLIB, THIRDPARTY, ASTROPY, FIRSTPARTY, LOCALFOLDER
 
 [coverage:run]
 omit =
-  sunkit_instruments/conftest.py
-  sunkit_instruments/cython_version*
-  sunkit_instruments/*setup*
-  sunkit_instruments/extern/*
-  sunkit_instruments/*/tests/*
-  sunkit_instruments/version*
-  sunkit_instruments/__init__*
-  sunkit_instruments/data/sample.py
-  sunkit_instruments/data/_sample.py
+  */sunkit_instruments/__init__*
+  */sunkit_instruments/*/tests/*
+  */sunkit_instruments/*setup*
   */sunkit_instruments/conftest.py
   */sunkit_instruments/cython_version*
-  */sunkit_instruments/*setup*
+  */sunkit_instruments/data/_sample.py
+  */sunkit_instruments/data/sample.py
   */sunkit_instruments/extern/*
-  */sunkit_instruments/*/tests/*
   */sunkit_instruments/version*
-  */sunkit_instruments/__init__*
-  */sunkit_instruments/data/sample.py
-  */sunkit_instruments/data/_sample.py
+  sunkit_instruments/__init__*
+  sunkit_instruments/*/tests/*
+  sunkit_instruments/*setup*
+  sunkit_instruments/conftest.py
+  sunkit_instruments/cython_version*
+  sunkit_instruments/data/_sample.py
+  sunkit_instruments/data/sample.py
+  sunkit_instruments/extern/*
+  sunkit_instruments/version*
 
 [coverage:report]
 exclude_lines =

setup.py

@@ -5,21 +5,6 @@
 
 from setuptools.config import read_configuration
 
-################################################################################
-# Actual setup.py content
-################################################################################
-
-VERSION_TEMPLATE = """
-# Note that we need to fall back to the hard-coded version if either
-# setuptools_scm can't be imported or setuptools_scm can't determine the
-# version, so we catch the generic 'Exception'.
-try:
-    from setuptools_scm import get_version
-    __version__ = get_version(root='..', relative_to=__file__)
-except Exception:
-    __version__ = '{version}'
-""".lstrip()
-
 ################################################################################
 # Programmatically generate some extras combos.
 ################################################################################
@@ -34,7 +19,7 @@
 # Concatenate all the values together for 'all'
 extras['all'] = list(chain.from_iterable(ex_extras.values()))
 
-setup(extras_require=extras,
-      use_scm_version={'write_to': os.path.join('sunkit_instruments', 'version.py'),
-                       'write_to_template': VERSION_TEMPLATE},
-      )
+setup(
+    extras_require=extras,
+    use_scm_version={'write_to': os.path.join('sunkit_instruments', '_version.py')}
+)

sunkit_instruments/__init__.py

@@ -9,15 +9,11 @@
 """
 import sys
 
+from .version import version as __version__  # NOQA
+
 # Enforce Python version check during package import.
 __minimum_python_version__ = "3.7"
 
-try:
-    from .version import __version__
-except ImportError:
-    print("version.py not found, please reinstall sunkit_instruments.")
-    __version__ = "unknown"
-
 
 class UnsupportedPythonError(Exception):
     """

sunkit_instruments/_dev/__init__.py

@@ -0,0 +1,6 @@
+"""
+This package contains utilities that are only used when developing drms in a
+copy of the source repository.
+These files are not installed, and should not be assumed to exist at
+runtime.
+"""

sunkit_instruments/_dev/scm_version.py

@@ -0,0 +1,12 @@
+# Try to use setuptools_scm to get the current version; this is only used
+# in development installations from the git repository.
+import os.path
+
+try:
+    from setuptools_scm import get_version
+
+    version = get_version(root=os.path.join('..', '..'), relative_to=__file__)
+except ImportError:
+    raise ImportError('setuptools_scm not installed')
+except Exception as e:
+    raise ValueError(f'setuptools_scm broken with {e}')

sunkit_instruments/lyra/tests/test_lyra.py

@@ -63,7 +63,7 @@ def test_split_series_using_lytaf():
     assert len(split) == 4
     assert is_time_equal(split[0]['subtimes'][0], parse_time((2010, 6, 13, 2, 0)))
     assert is_time_equal(split[0]['subtimes'][-1], parse_time((2010, 6, 13, 2, 7, 2)))
-    assert is_time_equal(split[3]['subtimes'][0], parse_time((2010, 6, 13, 2, 59, 42)))
+    assert is_time_equal(split[3]['subtimes'][0], parse_time((2010, 6, 13, 2, 59, 41)))
     assert is_time_equal(split[3]['subtimes'][-1], parse_time((2010, 6, 13, 2, 59, 58)))
 
     # Test case when no LYTAF events found in time series.