Merge pull request #70 from lsst-ts/tickets/DM-40054

Update MTAOS to remove usage of flake8 and black pytest plugins.

.github/workflows/changelog.yaml

@@ -0,0 +1,19 @@
+name: ChangelogUpdated
+on:
+ pull_request:
+ types: [assigned, opened, synchronize, reopened, labeled, unlabeled]
+ branches:
+ - develop
+jobs:
+ build:
+ name: Check Actions
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v1
+ - name: Changelog check
+ uses: Zomzog/[email protected]
+ with:
+ fileName: doc/versionHistory.rst
+ checkNotification: Simple
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/lint.yaml

@@ -0,0 +1,25 @@
+name: lint
+
+on:
+ - push
+ - pull_request
+
+jobs:
+ lint:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+
+ - name: Set up Python
+ uses: actions/setup-python@v2
+ with:
+ python-version: '3.10'
+
+ - name: Install
+ run: |
+ $CONDA/bin/conda install -c lsstts ts-pre-commit-config -y
+ $CONDA/bin/conda install -c conda-forge pre-commit -y
+ $CONDA/bin/generate_pre_commit_conf
+
+ - name: Run pre commit checks
+ run: $CONDA/bin/pre-commit run --all

.gitignore

@@ -20,4 +20,8 @@ pytest_session.txt
 
 # Mac related files
 .DS_Store
-.hypothesis/
+.hypothesis/
+.pre-commit-config.yaml
+.flake8
+.isort.cfg
+.mypy.ini

.ts_pre_commit_config.yaml

@@ -0,0 +1,6 @@
+check-yaml: true
+check-xml: true
+black: true
+flake8: true
+isort: true
+mypy: false

Jenkinsfile

@@ -55,9 +55,6 @@ pipeline {
  dir(env.WORKSPACE + '/ts_mtaos') {
  checkout scm
  }
- dir(env.WORKSPACE + '/phosim_utils') {
- git branch: 'main', url: 'https://github.com/lsst-dm/phosim_utils.git'
- }
  dir(env.WORKSPACE + '/ts_wep') {
  git branch: "${BRANCH}", url: 'https://github.com/lsst-ts/ts_wep.git'
  }
@@ -78,11 +75,7 @@ pipeline {
  cd ${env.SAL_USERS_HOME} && { curl -O ${env.PLANTUML_URL} ; cd -; }
  pip install sphinxcontrib-plantuml
 
- cd phosim_utils/
- setup -k -r . -t ${env.STACK_VERSION}
- scons
-
- cd ../ts_wep/
+ cd ${env.WHOME}/ts_wep/
  setup -k -r .
  scons python
 
@@ -112,16 +105,19 @@ pipeline {
  set +x
  source ${env.SAL_SETUP_FILE}
 
- cd phosim_utils/
- setup -k -r . -t ${env.STACK_VERSION}
-
- cd ../ts_wep/
+ cd ${env.WHOME}/ts_wep/
  setup -k -r .
 
- cd ../ts_ofc/
+ echo Checkout wep lfs data
+ git lfs install || echo git lfs install FAILED
+ git lfs fetch --all || echo git lfs fetch FAILED
+ git lfs checkout || echo git lfs checkout FAILED
+ 
+
+ cd ${env.WHOME}/ts_ofc/
  setup -k -r .
 
- cd ../ts_mtaos/
+ cd ${env.WHOME}/ts_mtaos/
  setup -k -r .
 
  # Exclude integration tests from the initial run. 
@@ -142,16 +138,13 @@ pipeline {
  set +x
  source ${env.SAL_SETUP_FILE}
 
- cd phosim_utils/
- setup -k -r . -t ${env.STACK_VERSION}
-
- cd ../ts_wep/
+ cd ${env.WHOME}/ts_wep/
  setup -k -r .
 
- cd ../ts_ofc/
+ cd ${env.WHOME}/ts_ofc/
  setup -k -r .
 
- cd ../ts_mtaos/
+ cd ${env.WHOME}/ts_mtaos/
  setup -k -r .
 
  package-docs build

bin/mtaos

@@ -33,7 +33,9 @@ class MTAOSCommander(salobj.CscCommander):
  self.mtaos_remote = salobj.Remote(
  domain=self.remote.salinfo.domain, name="MTAOS"
  )
- self.mtaos_remote.evt_settingsApplied = functools.partial(self.settings_callback)
+ self.mtaos_remote.evt_settingsApplied = functools.partial(
+ self.settings_callback
+ )
 
  self.mtaos_remote.tel_wepDuration.callback = functools.partial(
  self.duration_callback, name="wepDuration"

doc/conf.py

@@ -3,20 +3,20 @@
 This configuration only affects single-package Sphinx documentation builds.
 """
 
-from documenteer.conf.pipelinespkg import *
-import lsst.ts.mtaos
+import lsst.ts.mtaos # noqa
+from documenteer.conf.pipelinespkg import * # noqa
 
 project = "ts_mtaos"
-html_theme_options["logotext"] = project
+html_theme_options["logotext"] = project # noqa
 html_title = project
 html_short_title = project
 doxylink = {} # Avoid warning: Could not find tag file _doxygen/doxygen.tag
 
-intersphinx_mapping["ts_xml"] = ("https://ts-xml.lsst.io", None)
-intersphinx_mapping["ts_salobj"] = ("https://ts-salobj.lsst.io", None)
+intersphinx_mapping["ts_xml"] = ("https://ts-xml.lsst.io", None) # noqa
+intersphinx_mapping["ts_salobj"] = ("https://ts-salobj.lsst.io", None) # noqa
 
 # Support the sphinx extension of plantuml
-extensions.append("sphinxcontrib.plantuml")
+extensions.append("sphinxcontrib.plantuml") # noqa
 
 # Put the path to plantuml.jar
 plantuml = "java -jar /home/saluser/plantuml.jar"

doc/versionHistory.rst

@@ -2,6 +2,14 @@
 Version History
 ===============
 
+v0.12.1
+-------
+
+* Add support for ts-pre-commit-config.
+* Update package setup files.
+* Add git workflows to check version history is updated and linting.
+* Run isort.
+
 v0.12.0
 -------
 

pyproject.toml

@@ -0,0 +1,34 @@
+[build-system]
+requires = [ "setuptools", "setuptools_scm" ]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ts_mtaos"
+description = "Main Telescope Active Optical System."
+license = { text = "GPL" }
+classifiers = [ "Programming Language :: Python :: 3" ]
+urls = { documentation = "https://ts-mtaos.lsst.io", repository = "https://github.com/lsst-ts/ts_mtaos" }
+dynamic = [ "version" ]
+
+[tool.setuptools.dynamic]
+version = { attr = "setuptools_scm.get_version" }
+
+[tool.setuptools.packages.find]
+where = [ "python" ]
+
+[project.scripts]
+run_mtaos = "lsst.ts.mtaos:run_mtaos"
+
+[tool.setuptools_scm]
+write_to = "python/lsst/ts/mtaos/version.py"
+write_to_template = """
+# Generated by setuptools_scm
+__all__ = ["__version__"]
+__version__ = "{version}"
+"""
+
+[tool.pytest.ini_options]
+asyncio_mode = "auto"
+
+[project.optional-dependencies]
+dev = ["documenteer[pipelines]"]

python/lsst/ts/mtaos/__init__.py

@@ -27,9 +27,9 @@
 except ImportError:
  __version__ = "?"
 
-from .wavefront_collection import *
 from .config import *
 from .config_schema import *
 from .model import *
-from .utility import *
 from .mtaos import *
+from .utility import *
+from .wavefront_collection import *

python/lsst/ts/mtaos/config.py

@@ -21,8 +21,9 @@
 
 __all__ = ["Config"]
 
-from collections import namedtuple
 import warnings
+from collections import namedtuple
+
 import yaml
 
 from . import utility

python/lsst/ts/mtaos/model.py

@@ -21,41 +21,35 @@
 
 __all__ = ["Model"]
 
-import os
-import copy
-import yaml
-import shutil
 import asyncio
+import concurrent.futures
+import contextlib
+import copy
+import functools
 import logging
+import os
+import shutil
 import tempfile
-import functools
-import contextlib
-import concurrent.futures
-
-import numpy as np
-
 from typing import Optional
 
+import numpy as np
+import yaml
+from lsst.afw.image import VisitInfo
+from lsst.daf import butler as dafButler
 from lsst.ts.ofc import OFC
-from lsst.ts.utils import make_done_future
 from lsst.ts.salobj import DefaultingValidator
-
-from lsst.afw.image import VisitInfo
+from lsst.ts.utils import make_done_future
+from lsst.ts.wep.utility import writePipetaskCmd
 
 from .config_schema import (
  CWFS_PIPELINE_CONFIG,
- WEP_HEADER_CONFIG,
- ISR_CONFIG,
  GENERATE_DONUT_CATALOG_CONFIG,
+ ISR_CONFIG,
  SCIENCE_SENSOR_PIPELINE_CONFIG,
+ WEP_HEADER_CONFIG,
 )
-
+from .utility import define_visit, get_formatted_corner_wavefront_sensors_ids, timeit
 from .wavefront_collection import WavefrontCollection
-from .utility import define_visit, timeit, get_formatted_corner_wavefront_sensors_ids
-
-from lsst.ts.wep.utility import writePipetaskCmd
-
-from lsst.daf import butler as dafButler
 
 
 class Model:

python/lsst/ts/mtaos/mtaos.py

@@ -21,28 +21,22 @@
 
 __all__ = ["MTAOS"]
 
-import eups
-import yaml
-import typing
-import inspect
 import asyncio
+import inspect
 import logging
+import typing
 import warnings
 
-from astropy import units as u
-
+import eups
 import numpy as np
-
+import yaml
+from astropy import units as u
 from lsst.ts import salobj
 from lsst.ts.idl.enums.MTAOS import FilterType
 from lsst.ts.ofc import OFCData
 from lsst.ts.utils import astropy_time_from_tai_unix
 
-from . import CONFIG_SCHEMA, TELESCOPE_DOF_SCHEMA
-from . import Config
-from . import Model
-from . import utility
-from . import __version__
+from . import CONFIG_SCHEMA, TELESCOPE_DOF_SCHEMA, Config, Model, __version__, utility
 
 try:
  from lsst.ts.ofc import __version__ as __ofc_version__

python/lsst/ts/mtaos/utility.py

@@ -36,25 +36,23 @@
  "define_visit",
 ]
 
+import asyncio
+import logging
 import os
 import re
 import time
 import typing
-import asyncio
-import logging
-
-from logging.handlers import RotatingFileHandler
 from enum import Enum, auto
+from logging.handlers import RotatingFileHandler
 from pathlib import Path
 
-from lsst.utils import getPackageDir
 from lsst.daf.butler import Butler
 from lsst.obs.base import DefineVisitsTask, Instrument
 from lsst.obs.lsst.translators.lsstCam import LsstCamTranslator
-
-from lsst.ts.salobj import parse_idl
 from lsst.ts.idl import get_idl_dir
+from lsst.ts.salobj import parse_idl
 from lsst.ts.wep.utility import CamType
+from lsst.utils import getPackageDir
 
 
 class WEPWarning(Enum):

python/lsst/ts/mtaos/wavefront_collection.py

@@ -21,9 +21,10 @@
 
 __all__ = ["WavefrontCollection"]
 
-import numpy as np
 from collections import deque
 
+import numpy as np
+
 
 class WavefrontCollection(object):
  def __init__(self, maxLeng):