Merge pull request #568 from ICB-DCM/develop

Release 0.12.4

Author: yannikschaelte

.flake8

@@ -16,9 +16,9 @@ per-file-ignores =
   # Imported but unused
   */__init__.py:F401
   # Print
-  */cli.py:T001
-  pyabc/storage/migrate.py:T001
+  */cli.py:T201
+  pyabc/storage/migrate.py:T201
   # Print and asserts
-  test*/*.py:T001,S101
+  test*/*.py:T201,S101
   # Module level import not at top of file
   test/external/test_pyjulia.py:E402

.pre-commit-config.yaml

@@ -11,7 +11,7 @@
 
 repos:
 - repo: https://github.com/psf/black
-  rev: 22.1.0
+  rev: 22.3.0
   hooks:
   - id: black
     description: The uncompromising code formatter
@@ -34,7 +34,7 @@ repos:
       args: [--py36-plus]
     - id: nbqa-isort
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.2.0
+  rev: v4.2.0
   hooks:
   - id: check-yaml
     description: Check yaml files for parseable syntax

CHANGELOG.rst

@@ -8,6 +8,16 @@ Release Notes
 ...........
 
 
+0.12.4 (2022-05-05)
+-------------------
+
+Minor:
+
+* Move near-zero population weight to warning (#563)
+* Improve test installation instructions;
+  fix for updates of flake8-print and black (#567)
+
+
 0.12.3 (2022-04-05)
 -------------------
 

CONTRIBUTE.rst

@@ -19,6 +19,8 @@ get your work merged, please:
 3. check that the documentation is up-to-date,
 4. request a code review from the main developers.
 
+.. _environment:
+
 Environment
 -----------
 
@@ -30,8 +32,8 @@ via::
 Pre-commit hooks
 ~~~~~~~~~~~~~~~~
 
-Firstly, this installs a `pre-commit <https://pre-commit.com/>`_ tool.
-To add those hooks to the `.git` folder of your local clone such that they are
+First, this installs a `pre-commit <https://pre-commit.com/>`_ tool.
+To add those hooks to the ``.git`` folder of your local clone such that they are
 run on every commit, run::
 
     pre-commit install
@@ -43,7 +45,7 @@ once as usually only the diff is checked. The configuration is specified in
 Tox
 ~~~
 
-Secondly, this installs the virtual testing tool
+Second, this installs the virtual testing tool
 `tox <https://tox.readthedocs.io/en/latest/>`_, which we use for all tests,
 format and quality checks. Its configuration is specified in ``tox.ini``.
 To run it locally, simply execute::
@@ -53,6 +55,15 @@ To run it locally, simply execute::
 with optional ``-e`` options specifying the environments to run, see
 ``tox.ini`` for details.
 
+Extra dependencies
+~~~~~~~~~~~~~~~~~~
+
+Not all dependencies in particular of tests and documentation are managed via
+tox, e.g. installations of R and Julia, pandoc, and AMICI dependencies.
+To set these up locally, see e.g. ``.github/workflows/ci.yml`` and
+``.github/workflows/install_deps.sh`` (which can also be invoked locally)
+on how these are installed on GitHub Actions.
+
 GitHub Actions
 ~~~~~~~~~~~~~~
 
@@ -79,7 +90,8 @@ and then compile the documentation via::
 
 The documentation is then under ``doc/_build``.
 
-Alternatively, the documentation can be compiled and tested via a single line::
+Alternatively, the documentation can be compiled and tested via a single
+command::
 
     tox -e doc
 
@@ -101,11 +113,17 @@ Run them locally via e.g.::
     tox -e base
 
 with ``base`` covering basic tests, but some parts (``external,petab,...``)
-being in separate subfolders. This boils mostly down to e.g.::
+are in separate subfolders.
+Some dependencies are not managed via tox, see the above
+:ref:`environment` section.
+
+Tox basically mostly executes pytest on subsets of the tests, e.g.::
 
     pytest test/base
 
-You can also run only specific tests.
+pytest (install via ``pip install pytest``) can also be invoked directly
+like this, but may then require various further dependencies,
+see the environments in ``tox.ini``.
 
 Unit tests can be written with `pytest <https://docs.pytest.org/en/latest/>`_
 or `unittest <https://docs.python.org/3/library/unittest.html>`_.

pyabc/population.py

@@ -413,7 +413,13 @@ def normalize_weights(self):
         weights by the same factor ensures that weights stay comparable.
         """
         total_weight_accepted = sum(p.weight for p in self.accepted_particles)
-        if np.isclose(total_weight_accepted, 0):
+
+        if np.isclose(total_weight_accepted, 0.0):
+            logger.warning(
+                f"The total population weight {total_weight_accepted} is "
+                "close to zero, which can be numerically problematic"
+            )
+        if total_weight_accepted == 0.0:
             raise AssertionError("The total population weight is zero")
         for p in self.all_particles:
             p.weight /= total_weight_accepted

pyabc/sge/db.py

@@ -64,7 +64,7 @@ def wait_for_job(self, ID, max_run_time_h):
             job_start_time = results[0][1]
             # job took to long
             if not within_time(job_start_time, max_run_time_h):
-                print('Job ' + str(ID) + ' timed out.')  # noqa: T001
+                print('Job ' + str(ID) + ' timed out.')  # noqa: T201
                 return False  # job took too long
             else:  # still time left
                 return True

pyabc/sge/test_sge.py

@@ -8,14 +8,14 @@ def f(x):
         sleep(30)
         return x * 2
 
-    print("Start sge test", flush=True)  # noqa: T001
+    print("Start sge test", flush=True)  # noqa: T201
     sge = SGE(priority=0, memory="1G", name="test", time_h=1)
 
-    print("Do map", flush=True)  # noqa: T001
+    print("Do map", flush=True)  # noqa: T201
     res = sge.map(f, [1, 2, 3, 4])
 
-    print("Got results", flush=True)  # noqa: T001
+    print("Got results", flush=True)  # noqa: T201
     if res != [2, 4, 6, 8]:
         raise AssertionError("Wrong result, got {}".format(res))
 
-    print("Finished", flush=True)  # noqa: T001
+    print("Finished", flush=True)  # noqa: T201

pyabc/version.py

@@ -1 +1 @@
-__version__ = '0.12.3'
+__version__ = '0.12.4'

tox.ini

@@ -150,14 +150,14 @@ skip_install = true
 deps =
     # TODO unfix when bandit dep fixed
     bandit < 1.7.3
-    black >= 22.1.0
+    black >= 22.3.0
     flake8 >= 3.8.3
     flake8-bandit >= 2.1.2
     flake8-bugbear >= 20.1.4
     flake8-colors >= 0.1.6
     #flake8-commas >= 2.0.0
     flake8-comprehensions >= 3.2.3
-    flake8-print >= 3.1.4
+    flake8-print >= 5.0.0
     flake8-black >= 0.2.3
     flake8-isort >= 4.0.0
     # flake8-docstrings >= 1.5.0