asimov - pypi Package Compare versions

Comparing version 0.5.7 to 0.5.8

.gitlab-ci.yml

@@ -39,22 +39,2 @@ image: python:3.9
 
-test-python-36:
-  stage: test
-  image: python:3.6
-  script:
-  - git config --global user.email "[e-mail]"
-  - git config --global user.name "Your Name"
-  - pip install -r requirements.txt
-  - python setup.py install
-  - python -m unittest discover tests/
-
-test-python-37:
-  stage: test
-  image: python:3.7
-  script:
-  - git config --global user.email "[e-mail]"
-  - git config --global user.name "Your Name"
-  - pip install -r requirements.txt
-  - python setup.py install
-  - python -m unittest discover tests/
-
 test-python-38:
@@ -105,2 +85,27 @@ stage: test
 
+test-python-311:
+  stage: test
+  allow_failure: True  
+  image: python:3.11
+  script:
+    - git config --global user.email "[e-mail]"
+    - git config --global user.name "Your Name"
+    - pip install -r requirements.txt
+    - pip install coverage
+    - python setup.py install
+    - python -m unittest discover tests/
+
+test-python-312:
+  stage: test
+  allow_failure: True
+  image: python:3.12
+  script:
+    - git config --global user.email "[e-mail]"
+    - git config --global user.name "Your Name"
+    - pip install -r requirements.txt
+    - pip install coverage
+    - python setup.py install
+    - python -m unittest discover tests/
+    
+    
 # Build docs for multiple code versions
@@ -107,0 +112,0 @@ pages:

asimov.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: asimov
-Version: 0.5.7
+Version: 0.5.8
 Summary: A Python package for managing and interacting with data analysis jobs.
@@ -5,0 +5,0 @@ Home-page: https://git.ligo.org/asimov/asimov

asimov/cli/application.py

@@ -107,4 +107,16 @@ """
             hook.load()(ledger).run(event)
+            click.echo(
+                click.style("●", fg="green")
+                + f"{event} has been applied."
+            )
 
+            break
+    else:
+        click.echo(
+            click.style("●", fg="red")
+            + f"No hook found matching {hookname}. "
+            f"Installed hooks are {', '.join(discovered_hooks.names)}"
+        )
 
+
 @click.command()
@@ -111,0 +123,0 @@ @click.option("--file", "-f", help="Location of the file containing the ledger items.")

asimov/cli/monitor.py

@@ -123,3 +123,3 @@ import shutil
 
-    for event in ledger.get_event(event):
+    for event in sorted(ledger.get_event(event), key=lambda e: e.name):
         stuck = 0
@@ -126,0 +126,0 @@ running = 0

asimov/cli/report.py

@@ -165,3 +165,3 @@ """
     """
-    for event in current_ledger.get_event(event):
+    for event in sorted(current_ledger.get_event(event), key=lambda e: e.name):
         click.secho(f"{event.name:30}", bold=True)
@@ -168,0 +168,0 @@ if len(event.productions) > 0:

asimov/cli/review.py

 """
 Review functions for asimov events.
 """
+
 import os
@@ -28,16 +29,37 @@
     """
+    valid = {"REJECTED", "APPROVED", "PREFERRED", "DEPRECATED"}
+    events = current_ledger.get_event(event)
+    if events is None:
+        click.echo(
+            click.style("●", fg="red") + f" Could not find an event called {event}"
+        )
+    else:
+        for event in events:
+            production = [
+                production_o
+                for production_o in event.productions
+                if production_o.name == production
+            ][0]
+            click.secho(event.name, bold=True)
 
-    for event in current_ledger.get_event(event):
-        production = [
-            production_o
-            for production_o in event.productions
-            if production_o.name == production
-        ][0]
-        click.secho(event.name, bold=True)
-        click.secho(production.name)
-        message = ReviewMessage(message=message, status=status, production=production)
-        production.review.add(message)
+            if status.upper() in valid:
+                message = ReviewMessage(
+                    message=message, status=status, production=production
+                )
+                production.review.add(message)
+            else:
+                click.echo(
+                    click.style("●", fg="red")
+                    + f" Did not understand the review status {status.lower()}."
+                    + " The review status must be one of "
+                    + "{APPROVED, REJECTED, PREFERRED, DEPRECATED}"
+                )
 
-        if hasattr(event, "issue_object"):
-            production.event.update_data()
+            if hasattr(event, "issue_object"):
+                production.event.update_data()
+            current_ledger.update_event(event)
+            click.echo(
+                click.style("●", fg="green")
+                + f" {event.name}/{production.name} {status.lower()}"
+            )
 
@@ -52,6 +74,4 @@
     """
-    if isinstance(event, str):
-        event = [event]
     for event in current_ledger.get_event(event):
-        click.secho(event.title, bold=True)
+        click.secho(event.name, bold=True)
         if production:
@@ -66,4 +86,4 @@ productions = [
             click.secho(f"\t{production.name}", bold=True)
-            if "review" in production.meta:
-                click.echo(production.meta["review"])
+            if production.review:
+                click.echo(f"\t\t {production.review.status.lower()}")
             else:
@@ -70,0 +90,0 @@ click.secho("\t\tNo review information exists for this production.")

asimov/configs/bayeswave.ini

@@ -30,3 +30,3 @@ ;
 [engine]
-install_path={{ config["pipelines"]["environment"] }}
+install_path={{ scheduler['environment'] | default: config["pipelines"]["environment"] }}
 megaplot=%(install_path)s/bin/megaplot.py
@@ -33,0 +33,0 @@ bayeswave=%(install_path)s/bin/BayesWave

asimov/configs/bilby.ini

@@ -177,3 +177,3 @@ {%- if production.event.repository -%}
 ################################################################################
-analysis-executable={{ config['pipelines']['environment'] }}/bin/bilby_pipe_analysis
+analysis-executable={{ scheduler['environment'] | default: config['pipelines']['environment'] }}/bin/bilby_pipe_analysis
 environment-variables={{ scheduler['environment variables'] | default: "{'HDF5_USE_FILE_LOCKING': False, 'OMP_NUM_THREADS'=1, 'OMP_PROC_BIND'=False}" }}
@@ -180,0 +180,0 @@

asimov/event.py

@@ -612,2 +612,4 @@ """
         # Update with the event and project defaults
+        if "ledger" in self.event.meta:
+            self.event.meta.pop("ledger")
         self.meta = update(self.meta, deepcopy(self.event.meta))
@@ -714,3 +716,3 @@ if "productions" in self.meta:
         if "reference frequency" in self.meta["likelihood"]:
-            self.logger.warn(
+            self.logger.warning(
                 "Found deprecated ref freq information, "
@@ -887,2 +889,5 @@ "moving to waveform area of ledger"
 
+        if "ledger" in self.event.meta:
+            self.event.meta.pop("ledger")
+
         defaults = update(defaults, deepcopy(self.event.meta))
@@ -889,0 +894,0 @@

asimov/ledger.py

@@ -55,2 +55,6 @@ """
         self.events = {ev["name"]: ev for ev in self.data["events"]}
+        self._all_events = [
+            Event(**self.events[event], ledger=self)
+            for event in self.events.keys()
+            ]
         self.data.pop("events")
@@ -151,5 +155,3 @@
         else:
-            return [
-                Event(**self.events[event], ledger=self) for event in self.events.keys()
-            ]
+            return self._all_events
 
@@ -156,0 +158,0 @@ def get_productions(self, event=None, filters=None):

asimov/pipeline.py

 """Defines the interface with generic analysis pipelines."""
+
 import configparser
@@ -334,5 +335,9 @@ import os
             calibration = [
-                os.path.abspath(os.path.join(self.production.repository.directory, cal))
-                if not cal[0] == "/"
-                else cal
+                (
+                    os.path.abspath(
+                        os.path.join(self.production.repository.directory, cal)
+                    )
+                    if not cal[0] == "/"
+                    else cal
+                )
                 for cal in self.production.meta["data"]["calibration"].values()
@@ -419,2 +424,11 @@ ]
 
+        if "keywords" in self.meta:
+            for key, argument in self.meta["keywords"]:
+                if argument is not None and len(key) > 1:
+                    command += [f"--{key}", f"{argument}"]
+                elif argument is not None and len(key) == 1:
+                    command += [f"-{key}", f"{argument}"]
+                else:
+                    command += [f"{key}"]
+
         with utils.set_directory(self.production.rundir):
@@ -433,3 +447,3 @@ with open(f"{self.production.name}_pesummary.sh", "w") as bash_file:
             print("-----------------")
-            print(command)
+            print(" ".join(command))
 
@@ -436,0 +450,0 @@ submit_description = {

CHANGELOG.rst

@@ -0,1 +1,25 @@
+0.5.8
+=====
+
+This is a bug-fix release, which does not introduce any new backwards-incompatible features, but provides a number of small quality-of-life improvements.
+These include bug-fixes to various aspects of the CLI, and improvements to make using the CLI easier.
+This release also allows keyword arguments to be specified more easily to PESummary, and allows the environment of bilby and bayeswave executables to be specified on a per-analysis basis.
+
+We have ceased testing 0.5.8 against python 3.6 and python 3.7, and will drop support for these entirely after the next release.
+
+Breaking changes
+----------------
+
+This release is not believed to introduce any backwards-incompatible changes.
+
+Merges
+------
+
++ `ligo!140 <https://git.ligo.org/asimov/asimov/-/merge_requests/140>`_: Change CLI outputs to list events in alphanumeric order.
++ `ligo!145 <https://git.ligo.org/asimov/asimov/-/merge_requests/145>`_: Adds an error message if an unavailable pipeline is requested by an analysis.
++ `ligo!149 <https://git.ligo.org/asimov/asimov/-/merge_requests/149>`_: Fixes errors with various parts of the analysis review CLI, and improves error and information messages.
++ `ligo!151 <https://git.ligo.org/asimov/asimov/-/merge_requests/151>`_: Adds a confirmation message when a plugin is used to apply a new event to a project.
++ `ligo!152 <https://git.ligo.org/asimov/asimov/-/merge_requests/152>`_: Allows keyword arguments to be specified for summarypages jobs via a blueprint.
++ `ligo!153 <https://git.ligo.org/asimov/asimov/-/merge_requests/153>`_: Allows the analysis executable to be explicitly set from a blueprint for bilby and bayeswave.
+
 0.5.7
@@ -2,0 +26,0 @@ =====

PKG-INFO

 Metadata-Version: 2.1
 Name: asimov
-Version: 0.5.7
+Version: 0.5.8
 Summary: A Python package for managing and interacting with data analysis jobs.
@@ -5,0 +5,0 @@ Home-page: https://git.ligo.org/asimov/asimov

tests/test_cli_manage.py

@@ -163,3 +163,3 @@ """
             for event in EVENTS:
-                    output = """bayeswave_pipe --trigger-time=1126259462.391 -r """
+                    output = """bayeswave_pipe --trigger-time=1126259462.391 --copy-frames --transfer-files -r """
                     self.assertTrue(output in result.output)
@@ -166,0 +166,0 @@

tests/test_review.py

@@ -5,2 +5,14 @@ import unittest
 import git
+
+from importlib import reload
+import contextlib
+import io
+from unittest.mock import patch
+
+from click.testing import CliRunner
+
+import asimov
+from asimov.event import Production
+from asimov.cli import review, project
+from asimov.ledger import YAMLLedger
 import asimov.event
@@ -11,2 +23,4 @@ from asimov.cli.project import make_project
 
+EVENTS = ["GW150914_095045", "GW190924_021846", "GW190929_012149", "GW191109_010717"]
+pipelines = {"bayeswave"}
 
@@ -102,1 +116,94 @@ TEST_YAML = """
         self.assertEqual(self.event.productions[0].review.to_dicts()[0]['status'], 'REJECTED')
+
+
+class ReviewCliTests(unittest.TestCase):
+    """Test the CLI interfaces for review."""
+
+    @classmethod
+    def setUpClass(cls):
+        cls.cwd = os.getcwd()
+
+    def tearDown(self):
+        os.chdir(self.cwd)
+        shutil.rmtree(f"{self.cwd}/tests/tmp/")
+    
+    def setUp(self):
+        os.makedirs(f"{self.cwd}/tests/tmp/project")
+        os.chdir(f"{self.cwd}/tests/tmp/project")
+        runner = CliRunner()
+        result = runner.invoke(project.init,
+                               ['Test Project', '--root', f"{self.cwd}/tests/tmp/project"])
+        assert result.exit_code == 0
+        assert result.output == '● New project created successfully!\n'
+        self.ledger = YAMLLedger(".asimov/ledger.yml")
+
+        f = io.StringIO()
+        with contextlib.redirect_stdout(f):
+            apply_page(file = "https://git.ligo.org/asimov/data/-/raw/main/defaults/production-pe.yaml", event=None, ledger=self.ledger)
+            apply_page(file = "https://git.ligo.org/asimov/data/-/raw/main/defaults/production-pe-priors.yaml", event=None, ledger=self.ledger)
+            for event in EVENTS:
+                for pipeline in pipelines:
+                    apply_page(file = f"https://git.ligo.org/asimov/data/-/raw/main/tests/{event}.yaml", event=None, ledger=self.ledger)
+                    apply_page(file = f"https://git.ligo.org/asimov/data/-/raw/main/tests/{pipeline}.yaml", event=event, ledger=self.ledger)
+
+    def test_add_review_to_event_reject(self):
+        """Check that the CLI can add an event review"""
+        with patch("asimov.current_ledger", new=YAMLLedger(".asimov/ledger.yml")):
+            reload(asimov)
+            reload(review)
+            runner = CliRunner()
+
+            for event in EVENTS:
+                result = runner.invoke(review.review,
+                                       ['add', event, "Prod0", "Rejected"])
+                self.assertTrue(f"{event}/Prod0 rejected" in result.output)     
+
+    def test_add_review_to_event_reject(self):
+        """Check that the CLI can add an event review"""
+        with patch("asimov.current_ledger", new=YAMLLedger(".asimov/ledger.yml")):
+            reload(asimov)
+            reload(review)
+            runner = CliRunner()
+
+            for event in EVENTS:
+                result = runner.invoke(review.review,
+                                       ['add', event, "Prod0", "Approved"])
+                self.assertTrue(f"{event}/Prod0 approved" in result.output)          
+
+    def test_add_review_to_event_unknown(self):
+        """Check that the CLI rejects an unknown review status"""
+        with patch("asimov.current_ledger", new=YAMLLedger(".asimov/ledger.yml")):
+            reload(asimov)
+            reload(review)
+            runner = CliRunner()
+
+            for event in EVENTS:
+                result = runner.invoke(review.review,
+                                       ['add', event, "Prod0", "Splorg"])
+                self.assertTrue(f"Did not understand the review status splorg" in result.output)                          
+
+    def test_show_review_no_review(self):
+        """Check that the CLI can show a review report with no reviews"""
+        with patch("asimov.current_ledger", new=YAMLLedger(".asimov/ledger.yml")):
+            reload(asimov)
+            reload(review)
+            runner = CliRunner()
+
+            for event in EVENTS:
+                result = runner.invoke(review.review,
+                                       ['status', event])
+                self.assertTrue(f"No review information exists for this production." in result.output)            
+
+    def test_show_review_with_review(self):
+        """Check that the CLI can show a review report with no reviews"""
+        with patch("asimov.current_ledger", new=YAMLLedger(".asimov/ledger.yml")):
+            reload(asimov)
+            reload(review)
+            runner = CliRunner()
+
+            for event in EVENTS:
+                result = runner.invoke(review.review,
+                                       ['add', event, "Prod0", "Approved"])                
+                result = runner.invoke(review.review,
+                                       ['status', event])
+                self.assertTrue(f"approved" in result.output)       

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