diff --git a/CHANGELOG.md b/CHANGELOG.md index 1c8fec1fa..4a534ce79 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -61,6 +61,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), #### Fixed +- New input files are now detected when the run config contains glob expressions [#646](https://github.com/askap-vast/vast-pipeline/pull/646). - Fixed a regression from pandas==1.4.0 that caused empty groups to be passed to an apply function in parallel association [#642](https://github.com/askap-vast/vast-pipeline/pull/642). - Fixed docs issue that stopped serializers and views being shown in the code reference [#627](https://github.com/askap-vast/vast-pipeline/pull/627). - Fixed broken links to external search results from NED by URI encoding source names [#633](https://github.com/askap-vast/vast-pipeline/pull/633). @@ -91,6 +92,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), #### List of PRs +- [#646](https://github.com/askap-vast/vast-pipeline/pull/646): fix: run config diff check now considers number of images. - [#638](https://github.com/askap-vast/vast-pipeline/pull/638): feat: Support defer loading of dataTables data. - [#641](https://github.com/askap-vast/vast-pipeline/pull/641): dep: Drop Python 3.7 and dependency refresh. - [#643](https://github.com/askap-vast/vast-pipeline/pull/643): fix: Addressed pandas DataFrame.append deprecation. diff --git a/poetry.lock b/poetry.lock index 8e850d39c..947fee85f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -46,7 +46,7 @@ tests = ["pytest", "pytest-asyncio", "mypy (>=0.800)"] [[package]] name = "astropy" -version = "5.0.1" +version = "5.0.2" description = "Astronomy and astrophysics core library" category = "main" optional = false @@ -59,11 +59,11 @@ pyerfa = ">=2.0" PyYAML = ">=3.13" [package.extras] -all = ["scipy (>=1.3)", "matplotlib (>=3.1,!=3.4.0)", "certifi", "dask", "h5py", "pyarrow (>=5.0.0)", "beautifulsoup4", "html5lib", "bleach", "pandas", "sortedcontainers", "pytz", "jplephem", "mpmath", "asdf (>=2.6)", "bottleneck", "ipython (>=4.2)", "pytest", "typing-extensions"] -docs = ["sphinx (<4)", "sphinx-astropy (>=1.6)", "pytest", "scipy (>=1.3)", "matplotlib (>=3.1,!=3.4.0)", "sphinx-changelog (>=1.1.0)"] +all = ["scipy (>=1.3)", "matplotlib (>=3.1,!=3.4.0)", "certifi", "dask", "h5py", "pyarrow (>=5.0.0)", "beautifulsoup4", "html5lib", "bleach", "pandas", "sortedcontainers", "pytz", "jplephem", "mpmath", "asdf (>=2.9.2)", "bottleneck", "ipython (>=4.2)", "pytest (>=7.0)", "typing-extensions (>=3.10.0.1)"] +docs = ["sphinx (<4)", "sphinx-astropy (>=1.6)", "pytest (>=7.0)", "scipy (>=1.3)", "matplotlib (>=3.1,!=3.4.0)", "sphinx-changelog (>=1.1.0)"] recommended = ["scipy (>=1.3)", "matplotlib (>=3.1,!=3.4.0)"] -test = ["pytest-astropy (>=0.9)", "pytest-astropy-header (!=0.2.0)", "pytest-xdist"] -test_all = ["pytest-astropy (>=0.9)", "pytest-xdist", "objgraph", "ipython (>=4.2)", "coverage", "skyfield (>=1.20)", "sgp4 (>=2.3)"] +test = ["pytest (>=7.0)", "pytest-doctestplus (>=0.12)", "pytest-astropy (>=0.9)", "pytest-astropy-header (!=0.2.0)", "pytest-xdist"] +test_all = ["pytest (>=7.0)", "pytest-doctestplus (>=0.12)", "pytest-astropy (>=0.9)", "pytest-xdist", "objgraph", "ipython (>=4.2)", "coverage", "skyfield (>=1.20)", "sgp4 (>=2.3)"] [[package]] name = "astroquery" @@ -355,7 +355,7 @@ python-versions = "*" [[package]] name = "cryptography" -version = "36.0.1" +version = "36.0.2" description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." category = "main" optional = false @@ -692,7 +692,7 @@ pyflakes = ">=2.3.0,<2.4.0" [[package]] name = "fonttools" -version = "4.29.1" +version = "4.30.0" description = "Tools to manipulate font files" category = "main" optional = false @@ -832,7 +832,7 @@ docs = ["sphinx"] [[package]] name = "griffe" -version = "0.13.2" +version = "0.14.0" description = "Signatures for entire Python programs. 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if config_diff: + config_diff = pipeline.config.check_prev_config_diff(p_run.n_images) + if not config_diff: logger.info( "The config file has either not changed since the" " previous run or other settings have changed such" diff --git a/vast_pipeline/pipeline/config.py b/vast_pipeline/pipeline/config.py index 71b20620f..f663a6dc2 100644 --- a/vast_pipeline/pipeline/config.py +++ b/vast_pipeline/pipeline/config.py @@ -1,7 +1,7 @@ from glob import glob import logging import os -from typing import Any, Dict, List +from typing import Any, Dict, List, Optional from django.contrib.auth.models import User from django.conf import settings @@ -507,25 +507,54 @@ def validate(self, user: User = None): if not os.path.exists(file): raise PipelineConfigError(f"{file} does not exist.") - def check_prev_config_diff(self) -> bool: + def count_images(self) -> int: + """Count the number of input images in the config. Assumes the config has been + validated and glob expressions have been resolved. + + Returns: + int: The number of input images in the config. + """ + n_images = 0 + for _, images in self._yaml.data["inputs"]["image"].items(): + n_images += len(images) + return n_images + + def check_prev_config_diff( + self, prev_n_images: int, prev_config: Optional["PipelineConfig"] = None + ) -> bool: """ Checks if the previous config file differs from the current config file. Used in add mode. Only returns true if the images are different and the other general settings are the same (the requirement for add mode). Otherwise False is returned. + Args: + prev_n_images (int): The number of input images in the previous run. If the + number of input images after resolving glob expressions is greater than + this value, the config is considered different. + Returns: `True` if images are different but general settings are the same, otherwise `False` is returned. """ - prev_config = PipelineConfig.from_file( - os.path.join(self["run"]["path"], "config_prev.yaml"), - label="previous run config", - ) - if self._yaml == prev_config._yaml: - return True + if prev_config is None: + prev_config = PipelineConfig.from_file( + os.path.join(self["run"]["path"], "config_prev.yaml"), + label="previous run config", + ) + + # count the input images in case the config uses glob expressions and new images + # have appeared on disk + n_images = self.count_images() + + # is the config unchanged, including the image count? + if self._yaml == prev_config._yaml and n_images == prev_n_images: + return False # are the input image files different? - images_changed = self["inputs"]["image"] != prev_config["inputs"]["image"] + images_changed = ( + self["inputs"]["image"] != prev_config["inputs"]["image"] + or n_images > prev_n_images + ) # are all the non-input file configs the same? config_dict = self._yaml.data @@ -535,8 +564,8 @@ def check_prev_config_diff(self) -> bool: settings_check = config_dict == prev_config_dict if images_changed and settings_check: - return False - return True + return True + return False def image_opts(self) -> Dict[str, Any]: """ diff --git a/vast_pipeline/tests/test_pipelineconfig.py b/vast_pipeline/tests/test_pipelineconfig.py index 894caf6a6..84083c76b 100644 --- a/vast_pipeline/tests/test_pipelineconfig.py +++ b/vast_pipeline/tests/test_pipelineconfig.py @@ -5,6 +5,7 @@ from django.conf import settings from django.contrib.auth.models import AnonymousUser from django.test import SimpleTestCase, override_settings +from pyfakefs.fake_filesystem_unittest import TestCase as FakeFsTestCase import strictyaml as yaml from vast_pipeline.management.commands.initpiperun import make_config_template @@ -20,8 +21,16 @@ PIPELINE_WORKING_DIR=os.path.join(TEST_ROOT, "pipeline-runs"), MAX_PIPERUN_IMAGES=10, ) -class CheckRunConfigValidationTest(SimpleTestCase): +class CheckRunConfigValidationTest(SimpleTestCase, FakeFsTestCase): def setUp(self): + # set up fake filesystem + self.setUpPyfakefs() + self.fs.add_real_directory( + os.path.join(settings.PIPELINE_WORKING_DIR, "basic-association") + ) + self.fs.add_real_file(PipelineConfig.TEMPLATE_PATH) + self.fs.add_real_directory("vast_pipeline/tests/data") + # load a base run configuration file self.config_path = os.path.join( settings.PIPELINE_WORKING_DIR, "basic-association", "config.yaml" @@ -185,6 +194,62 @@ def test_input_glob(self): pipeline_config_original._yaml.data, pipeline_config_globs._yaml.data ) + def test_diff_glob(self): + """Test that changes to the input files on disk trigger a config change for runs + that use glob expressions.""" + def gen_config(config_dict) -> PipelineConfig: + config_yaml = yaml.as_document(config_dict) + config = PipelineConfig(config_yaml) + config.validate() + return config + + # replace the inputs with glob expressions + self.config_dict["inputs"]["image"] = { + "glob": "vast_pipeline/tests/data/epoch??.fits" + } + self.config_dict["inputs"]["selavy"] = { + "glob": "vast_pipeline/tests/data/epoch??.selavy.components.txt" + } + self.config_dict["inputs"]["noise"] = { + "glob": "vast_pipeline/tests/data/epoch??.noiseMap.fits" + } + self.config_dict["inputs"]["background"] = { + "glob": "vast_pipeline/tests/data/epoch??.meanMap.fits" + } + pipeline_config_globs = gen_config(self.config_dict) + n_images = pipeline_config_globs.count_images() + + # Generate another pipeline config object using the same glob expressions as + # above. Contents will be the same as pipeline_config_globs. + pipeline_config_globs_nochange = gen_config(self.config_dict) + + # no change to config nor filesystem, diff check should return False + self.assertFalse( + pipeline_config_globs_nochange.check_prev_config_diff( + n_images, prev_config=pipeline_config_globs + ) + ) + + # add a new input files to the fake filesystem + for f in ( + "epoch00.fits", + "epoch00.meanMap.fits", + "epoch00.noiseMap.fits", + "epoch00.selavy.components.txt", + ): + self.fs.create_file(f"vast_pipeline/tests/data/{f}") + + # Generate another pipeline config object using the same glob expressions as + # above. Contents will be different as new inputs were added to the filesystem. + pipeline_config_globs_newfiles = gen_config(self.config_dict) + + # the config inputs should now be different + self.assertTrue( + pipeline_config_globs_newfiles.check_prev_config_diff( + n_images, prev_config=pipeline_config_globs + ) + ) + def test_input_multiple_globs(self): """Test multiple consecutive glob expressions""" config_yaml_original = yaml.as_document(self.config_dict)