ampycloud 0.6.0.dev0__tar.gz → 2.0.0__tar.gz

{ampycloud-0.6.0.dev0 → ampycloud-2.0.0}/AUTHORS

@@ -1,2 +1,3 @@
 Scientific Developers:
 - @fpavogt (Frédéric P.A. Vogt), frederic.vogt@meteoswiss.ch
+- @regDaniel (Daniel Regenass), daniel.regenass@meteoswiss.ch

{ampycloud-0.6.0.dev0 → ampycloud-2.0.0}/CHANGELOG

@@ -3,6 +3,33 @@ All notable changes to ampycloud will be documented in this file.
 The format is inspired from [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v2.0.0]
+### Added:
+ - [fpavogt, 2024-06-26] Add ability to trigger weekly tests manually.
+ - [fpavogt, 2024-04-16] Improve input data consistency check (fix #116).
+ - [regDaniel, 2024-04-09] Add flag for clouds above (MSA + MSA_HIT_BUFFER) and allow for NSC in METAR message.
+ - [fpavogt, 2024-03-26] Add option to reset only a single parameter.
+### Fixed:
+ - [srethore, 2024-04-23] Fix static types issues.
+ - [regDaniel, 2024-04-23] Fix deprecated github actions worklflow file
+ - [fpavogt, 2024-04-17] Fix #119
+ - [regDaniel, 2024-04-09] Minor adaptions to better comply with PEP standards.
+ - [fpavogt, 2024-03-26] Use "height" in "ft aal" throughout.
+### Changed:
+ - [fpavogt, 2024-06-25] Add support for numpy >2.0
+ - [fpavogt, 2024-04-28] Add a rogue point to the mock example.
+ - [fpavogt, 2024-03-25] Set the fluffiness boost to 2 (fixes #123).
+ - [fpavogt, 2024-03-23] Changed default mock dataset to be 900s long (instead of 2400s).
+
+## [v1.0.0]
+### Added:
+ - [regDaniel, 2023-11-09] Add minimum separation condition for grouping step.
+### Fixed:
+ - [regDaniel, 2023-11-09] Fix #107 (no more reporting of two layers at same height).
+### Changed:
+- [fpavogt, 2023-11-05] Updated version to 1.0.0 for first full release, incl. misc documentation changes.
+- [regDaniel, 2023-11-09] Changed min sep in layering from layer mean to layer base altitude.
+- [regDaniel, 2023-11-10] Refactoring (modularization) of metarize method.
 
 ## [v0.6.0.dev0]
 ### Added:
@@ -27,9 +54,6 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
  - [fpavogt, 2022-10-18] Cleanup pylint and error messages.
  - [fpavogt, 2022-10-18] Use min/max+padding to assess if slices are overlapping, instead of mean+std.
  - [fpavogt, 2022-10-18] Default value of OKTA_LIM8 is changed from 98 to 99.
-### Deprecated:
-### Removed:
-### Security:
 
 ## [v0.5.0.dev0]
 ### Fixed:

{ampycloud-0.6.0.dev0 → ampycloud-2.0.0}/CONTRIBUTING.md

@@ -2,15 +2,15 @@
 
 If you:
 
-*  :boom: want to **report a bug** with ampycloud: [jump here.](https://github.com/MeteoSwiss/ampycloud/issues)
-*  :question: have a **question** about ampycloud: [jump here instead.](https://github.com/MeteoSwiss/ampycloud/discussions)
-* :construction_worker: want to **contribute** to ampycloud (:heart_eyes: :tada:): read on !
+* :boom: want to **report a bug** with ampycloud: [jump here.](https://github.com/MeteoSwiss/ampycloud/issues)
+* :question: have a **question** about ampycloud: [jump here instead.](https://github.com/MeteoSwiss/ampycloud/discussions)
+* :construction_worker: want to **contribute** to ampycloud, read on !
 
 
 ## Table of contents
 
 - [Code of conduct](#code-of-conduct)
-- [Scope of ampycloud](#scope-of-ampycloud)
+- [Scope](#scope)
 - [Essential things to know about ampycloud for dev work](#essential-things-to-know-about-ampycloud-for-dev-work)
     - [Branching model](#branching-model)
     - [Installing from source](#installing-from-source)
@@ -23,7 +23,7 @@ If you:
     - [Documentation](#documentation)
     - [Testing](#testing)
     - [Plotting](#plotting)
-    - [Release mechanisms](#release-mechanisms)
+    - [Release mechanism](#release-mechanism)
 - [Less-Essential things to know about ampycloud for dev work](#less-essential-things-to-know-about-ampycloud-for-dev-work)
     - [Updating the copyright years](#updating-the-copyright-years)
 
@@ -31,10 +31,9 @@ If you:
 ## Code of conduct
 
 This project and everyone participating in it is governed by the [ampycloud Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code.
-Please report unacceptable behavior to [loris.foresti@meteoswiss.ch](mailto:loris.foresti@meteoswiss.ch) and/or [frederic.vogt@meteoswiss.ch](mailto:frederic.vogt@meteoswiss.ch).
+Please report unacceptable behavior to [loris.foresti@meteoswiss.ch](mailto:loris.foresti@meteoswiss.ch).
 
-
-## Scope of ampycloud
+## Scope
 
 Please be sure to read (and understand the implications) of the
 [scope of ampycloud](https://meteoswiss.github.io/ampycloud/index.html#scope-of-ampycloud).
@@ -86,9 +85,11 @@ Automated CI/CD checks are triggered upon Pull Requests being issued towards the
 * automatic publication of the Sphinx docs (for a PR to `master` only)
 * check that the code version was incremented (for PR to `master` only)
 
-To test the code with the latest Python developments, a `pytest-weeklz` workflow runs the
+To test the latest release of the code with the latest Python developments, a `pytest-weekly` workflow runs the
 ampycloud tests twice a week using the latest version of Python and of the ampycloud dependencies.
 
+:warning: This test is being run from the `master` branch. Pushing a bug fix to `develop` will not be sufficient to make it turn green - a new code release is necessary !
+
 There is another Github action responsible for publishing the code onto pypi, that gets triggered
 upon a new release or pre-release being published. See the ampycloud
 [release mechanisms](#release-mechanisms) for details.
@@ -293,7 +294,7 @@ def some_plot_function(...):
 With this decorator, all functions will automatically deploy the effects associated to the value of `dynamic.AMPYCLOUD_PRMS['MPL_STYLE']` which can take one of the following values:
 `['base', 'latex', 'metsymb']`.
 
-### Release mechanisms
+### Release mechanism
 
 When changes merged in the `develop` branch are stable and deemed *worthy*, follow these steps to
 create a new release of ampycloud:
@@ -325,13 +326,14 @@ create a new release of ampycloud:
    - on the [release page](https://github.com/MeteoSwiss/ampycloud/releases),
    - in the [README](https://github.com/MeteoSwiss/ampycloud/blob/develop/README.md) tags,
    - on [testpypi](https://test.pypi.org/project/ampycloud/) and [pypi](https://pypi.org/project/ampycloud/),
-   - on the [`gh-pages` branch](https://github.com/MeteoSwiss/ampycloud/tree/gh-pages), and
-   - in the [live documentation](https://MeteoSwiss.github.io/ampycloud).
+   - on the [`gh-pages` branch](https://github.com/MeteoSwiss/ampycloud/tree/gh-pages),
+   - in the [live documentation](https://MeteoSwiss.github.io/ampycloud), and
+   - on [Zenodo](https://zenodo.org/doi/10.5281/zenodo.8399683) (for which the connection to this repo is enabled from Zenodo itself, by the admins of the MeteoSwiss organization on Github).
 
 ## Less-Essential things to know about ampycloud for dev work
 
 ### Updating the copyright years
-The ampycloud copyright years may need to be updated if the development goes on beyond 2022. If so,
+The ampycloud copyright years may need to be updated if the development goes on beyond 2022 (which it already has 😉). If so,
 the copyright years will need to be manually updated in the following locations:
 
 * `docs/source/substitutions.rst` (the copyright tag)

{ampycloud-0.6.0.dev0 → ampycloud-2.0.0}/PKG-INFO

@@ -1,19 +1,22 @@
 Metadata-Version: 2.1
 Name: ampycloud
-Version: 0.6.0.dev0
-Summary: Characterization of cloud layers from ceilometer measurements
+Version: 2.0.0
+Summary: Determining the sky coverage fraction and base height of cloud layers usingceilometer data
 Home-page: https://meteoswiss.github.io/ampycloud
-Author: Frédéric P.A. Vogt
+Author: Frédéric P.A. Vogt, Daniel Regenass
 Author-email: frederic.vogt@meteoswiss.ch
 License: BSD-3-Clause
 Project-URL: Source, https://github.com/MeteoSwiss/ampycloud/
 Project-URL: Changelog, https://meteoswiss.github.io/ampycloud/changelog.html
 Project-URL: Issues, https://github.com/MeteoSwiss/ampycloud/issues
-Classifier: Development Status :: 3 - Alpha
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
 Classifier: License :: OSI Approved :: BSD License
-Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.9.0
 Description-Content-Type: text/markdown
 Provides-Extra: dev
@@ -22,6 +25,7 @@ License-File: AUTHORS
 
 # ampycloud
 
+[![DOI](https://zenodo.org/badge/435391098.svg)](https://zenodo.org/doi/10.5281/zenodo.8399683)
 [![github](https://img.shields.io/github/release/MeteoSwiss/ampycloud.svg)](https://github.com/MeteoSwiss/ampycloud/releases)
 [![last-commit](https://img.shields.io/github/last-commit/MeteoSwiss/ampycloud.svg?colorB=e6c000)](https://github.com/MeteoSwiss/ampycloud)
 [![issues](https://img.shields.io/github/issues/MeteoSwiss/ampycloud.svg?colorB=b4001e)](https://github.com/MeteoSwiss/ampycloud/issues)
@@ -38,7 +42,7 @@ For the full documentation, installation instructions, etc ..., go to: https://m
 
 ### License & Copyright
 
-ampycloud is released under the terms of **the 3-Clause BSD license**. The copyright (2021-2023) belongs to MeteoSwiss.
+ampycloud is released under the terms of **the 3-Clause BSD license**. The copyright (2021-2024) belongs to MeteoSwiss.
 
 ### Contributing to ampycloud
 

{ampycloud-0.6.0.dev0 → ampycloud-2.0.0}/README.md

@@ -1,5 +1,6 @@
 # ampycloud
 
+[![DOI](https://zenodo.org/badge/435391098.svg)](https://zenodo.org/doi/10.5281/zenodo.8399683)
 [![github](https://img.shields.io/github/release/MeteoSwiss/ampycloud.svg)](https://github.com/MeteoSwiss/ampycloud/releases)
 [![last-commit](https://img.shields.io/github/last-commit/MeteoSwiss/ampycloud.svg?colorB=e6c000)](https://github.com/MeteoSwiss/ampycloud)
 [![issues](https://img.shields.io/github/issues/MeteoSwiss/ampycloud.svg?colorB=b4001e)](https://github.com/MeteoSwiss/ampycloud/issues)
@@ -16,7 +17,7 @@ For the full documentation, installation instructions, etc ..., go to: https://m
 
 ### License & Copyright
 
-ampycloud is released under the terms of **the 3-Clause BSD license**. The copyright (2021-2023) belongs to MeteoSwiss.
+ampycloud is released under the terms of **the 3-Clause BSD license**. The copyright (2021-2024) belongs to MeteoSwiss.
 
 ### Contributing to ampycloud
 

{ampycloud-0.6.0.dev0 → ampycloud-2.0.0}/setup.py

@@ -1,5 +1,5 @@
 """
-Copyright (c) 2021-2022 MeteoSwiss, contributors listed in AUTHORS.
+Copyright (c) 2021-2024 MeteoSwiss, contributors listed in AUTHORS.
 
 Distributed under the terms of the 3-Clause BSD License.
 
@@ -35,9 +35,10 @@ setup(
         'Changelog': 'https://meteoswiss.github.io/ampycloud/changelog.html',
         'Issues': 'https://github.com/MeteoSwiss/ampycloud/issues'
     },
-    author="Frédéric P.A. Vogt",
+    author="Frédéric P.A. Vogt, Daniel Regenass",
     author_email="frederic.vogt@meteoswiss.ch",
-    description="Characterization of cloud layers from ceilometer measurements",
+    description="Determining the sky coverage fraction and base height of cloud layers using"
+    "ceilometer data",
     long_description=long_description,
     long_description_content_type="text/markdown",
     python_requires='>=3.9.0',
@@ -52,7 +53,7 @@ setup(
         "ruamel.yaml"
     ],
     extras_require={
-        'dev': ['sphinx', 'sphinx-rtd-theme', 'pylint', 'pytest']
+        'dev': ['sphinx', 'sphinx-rtd-theme', 'pylint', 'pytest', 'setuptools', 'mypy']
     },
     # Setup entry points to use ampycloud directly from a terminal
     entry_points={
@@ -63,7 +64,7 @@ setup(
         #   3 - Alpha
         #   4 - Beta
         #   5 - Production/Stable
-        'Development Status :: 3 - Alpha',
+        'Development Status :: 5 - Production/Stable',
         # Indicate who your project is intended for
         'Intended Audience :: Science/Research',
         'Topic :: Scientific/Engineering :: Atmospheric Science',
@@ -71,7 +72,10 @@ setup(
         'License :: OSI Approved :: BSD License',
         # Specify the Python versions you support here. In particular, ensure
         # that you indicate whether you support Python 2, Python 3 or both.
-        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
     ],
     # Let's make sure the parameter non-py files get included in the wheels on pypi.
     include_package_data=True

{ampycloud-0.6.0.dev0 → ampycloud-2.0.0}/src/ampycloud/cluster.py

@@ -10,7 +10,7 @@ Module contains: clustering tools
 
 # Import from Python
 import logging
-from typing import Union
+from typing import Optional, Union
 import numpy as np
 from sklearn.cluster import AgglomerativeClustering
 
@@ -23,7 +23,7 @@ logger = logging.getLogger(__name__)
 
 
 @log_func_call(logger)
-def agglomerative_cluster(data: np.ndarray, n_clusters: int = None,
+def agglomerative_cluster(data: np.ndarray, n_clusters: Union[int, None] = None,
                           metric: str = 'euclidean', linkage: str = 'single',
                           distance_threshold: Union[int, float] = 1) -> tuple:
     """ Function that wraps arround :py:class:`sklearn.cluster.AgglomerativeClustering`.
@@ -54,7 +54,7 @@ def agglomerative_cluster(data: np.ndarray, n_clusters: int = None,
 
 
 @log_func_call(logger)
-def clusterize(data: np.ndarray, algo: str = None, **kwargs: dict) -> tuple:
+def clusterize(data: np.ndarray, algo: Union[str, None] = None, **kwargs: dict) -> Optional[tuple]:
     """ Umbrella clustering routine, that provides a single access point to the different clustering
     algorithms.
 

{ampycloud-0.6.0.dev0 → ampycloud-2.0.0}/src/ampycloud/core.py

@@ -1,5 +1,5 @@
 """
-Copyright (c) 2021-2022 MeteoSwiss, contributors listed in AUTHORS.
+Copyright (c) 2021-2024 MeteoSwiss, contributors listed in AUTHORS.
 
 Distributed under the terms of the BSD-3-Clause license.
 
@@ -56,11 +56,11 @@ def copy_prm_file(save_loc: str = './', which: str = 'defaults') -> None:
     """
 
     # Let's take a look at the path I was given
-    save_loc = Path(save_loc)
+    given_path = Path(save_loc)
     # I won't create stuff for the users. ampycloud is not that nice.
-    if not save_loc.exists():
+    if not given_path.exists():
         raise AmpycloudError('save_loc does not appear to exist !')
-    if not save_loc.is_dir():
+    if not given_path.is_dir():
         raise AmpycloudError('save_loc does not appear to be a directory !')
 
     # Next, let's look at all the parameter files available ...
@@ -73,11 +73,11 @@ def copy_prm_file(save_loc: str = './', which: str = 'defaults') -> None:
     if (fname := f'ampycloud_{which}_prms.yml') not in ref_files:
         raise AmpycloudError(f'Parameter file {fname} not found.')
 
-    if (save_loc / fname).exists():
-        raise AmpycloudError(f'File {fname} already exists at save_loc={save_loc}')
+    if (given_path / fname).exists():
+        raise AmpycloudError(f'File {fname} already exists at save_loc={given_path}')
 
     # All looks good, let's copy the file
-    copy(ref_loc / fname, save_loc / fname)
+    copy(ref_loc / fname, given_path / fname)
 
 
 @log_func_call(logger)
@@ -131,9 +131,13 @@ def set_prms(pth: Union[str, Path]) -> None:
 
 
 @log_func_call(logger)
-def reset_prms() -> None:
+def reset_prms(which: Union[str, list, None] = None) -> None:
     """ Reset the ampycloud dynamic=scientific parameters to their default values.
 
+    Args:
+        which (str|list, optional): (list of) names of parameters to reset specifically.
+            If not set (by default), all parameters will be reset.
+
     Example:
         ::
 
@@ -148,12 +152,26 @@ def reset_prms() -> None:
 
     """
 
-    dynamic.AMPYCLOUD_PRMS = dynamic.get_default_prms()
+    if which is None:
+        dynamic.AMPYCLOUD_PRMS = dynamic.get_default_prms()
+        return
+
+    # Ok, reset the parameters one at a time
+    default_prms = dynamic.get_default_prms()
+
+    # Clean up which
+    which = [which] if isinstance(which, str) else which
+
+    for prm in which:
+        if prm not in default_prms.keys():
+            raise AmpycloudError(f'Unknown parameter name: {prm}')
+
+        dynamic.AMPYCLOUD_PRMS[prm] = default_prms[prm]
 
 
 @log_func_call(logger)
-def run(data: pd.DataFrame, prms: dict = None, geoloc: str = None,
-        ref_dt: Union[str, datetime] = None) -> CeiloChunk:
+def run(data: pd.DataFrame, prms: Union[dict, None] = None, geoloc: Union[str, None] = None,
+        ref_dt: Union[str, datetime, None] = None) -> CeiloChunk:
     """ Runs the ampycloud algorithm on a given dataset.
 
     Args:
@@ -179,7 +197,7 @@ def run(data: pd.DataFrame, prms: dict = None, geoloc: str = None,
 
     .. important ::
         ampycloud treats Vertical Visibility hits no differently than any other hit. Hence, it is up
-        to the user to adjust the Vertical Visibility hit altitude (and/or ignore some of them, for
+        to the user to adjust the Vertical Visibility hit height (and/or ignore some of them, for
         example) prior to feeding them to ampycloud, so that it can be used as a cloud hit.
 
     .. important::
@@ -193,7 +211,7 @@ def run(data: pd.DataFrame, prms: dict = None, geoloc: str = None,
 
     All the scientific parameters of the algorithm are set dynamically in the :py:mod:`.dynamic`
     module. From within a Python session all these parameters can be changed directly. For example,
-    to change the Minimum Sector Altitude, one would do:
+    to change the Minimum Sector Altitude (to be specified in ft aal), one would do:
     ::
 
         from ampycloud import dynamic
@@ -223,7 +241,7 @@ def run(data: pd.DataFrame, prms: dict = None, geoloc: str = None,
     The :py:class:`.data.CeiloChunk` instance returned by this function contains all the information
     associated to the ampycloud algorithm, inclduing the raw data and slicing/grouping/layering
     info. Its method :py:meth:`.data.CeiloChunk.metar_msg` provides direct access to the resulting
-    METAR-like message. Users that require the altitude, okta amount, and/or exact sky coverage
+    METAR-like message. Users that require the height, okta amount, and/or exact sky coverage
     fraction of layers can get them via the :py:attr:`.data.CeiloChunk.layers` class property.
 
     Example:
@@ -239,7 +257,7 @@ def run(data: pd.DataFrame, prms: dict = None, geoloc: str = None,
             # Generate the canonical demo dataset for ampycloud
             mock_data = mocker.canonical_demo_data()
 
-            # Run the ampycloud algorithm on it, setting the MSA to 10'000 ft
+            # Run the ampycloud algorithm on it, setting the MSA to 10'000 ft aal.
             chunk = ampycloud.run(mock_data, prms={'MSA':10000},
                                   geoloc='Mock data', ref_dt=datetime.now())