PyPI - pycellid - Versions diffs - 0.1__tar.gz → 0.2.0__tar.gz - Mend

pycellid 0.1tar.gz → 0.2.0tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (23) hide show

pycellid-0.2.0/CHANGELOG.rst +29 -0
pycellid-0.2.0/MANIFEST.in +5 -0
{pycellid-0.1/pycellid.egg-info → pycellid-0.2.0}/PKG-INFO +33 -23
{pycellid-0.1 → pycellid-0.2.0}/README.md +9 -8
{pycellid-0.1 → pycellid-0.2.0}/pycellid/__init__.py +1 -1
{pycellid-0.1 → pycellid-0.2.0}/pycellid/core.py +1 -1
{pycellid-0.1 → pycellid-0.2.0}/pycellid/io.py +2 -2
{pycellid-0.1 → pycellid-0.2.0/pycellid.egg-info}/PKG-INFO +33 -23
{pycellid-0.1 → pycellid-0.2.0}/pycellid.egg-info/SOURCES.txt +5 -2
pycellid-0.2.0/pycellid.egg-info/requires.txt +4 -0
pycellid-0.2.0/pyproject.toml +108 -0
pycellid-0.2.0/tests/test_core.py +417 -0
pycellid-0.2.0/tests/test_images.py +152 -0
pycellid-0.2.0/tests/test_io.py +339 -0
pycellid-0.1/CHANGELOG.rst +0 -2
pycellid-0.1/MANIFEST.in +0 -12
pycellid-0.1/pycellid.egg-info/requires.txt +0 -4
pycellid-0.1/setup.py +0 -87
{pycellid-0.1 → pycellid-0.2.0}/LICENSE +0 -0
{pycellid-0.1 → pycellid-0.2.0}/pycellid/images.py +0 -0
{pycellid-0.1 → pycellid-0.2.0}/pycellid.egg-info/dependency_links.txt +0 -0
{pycellid-0.1 → pycellid-0.2.0}/pycellid.egg-info/top_level.txt +0 -0
{pycellid-0.1 → pycellid-0.2.0}/setup.cfg +0 -0

pycellid-0.2.0/CHANGELOG.rst ADDED Viewed

@@ -0,0 +1,29 @@
+PyCellID Changelog
+===================
+Version (0.2.0)
+------------------
+- Packaging configuration moved to ``pyproject.toml`` (PEP 621);
+  ``setup.py`` and ``requirements/`` removed. Development dependencies
+  are now dependency groups (PEP 735): ``pip install -e . --group dev``.
+- Supported Python versions: 3.11 to 3.15 (3.8, 3.9 and 3.10 dropped).
+- Minimum dependencies: attrs 22.2, matplotlib 3.7, numpy 1.24, pandas 2.0.
+- CI rewritten: Python 3.11 to 3.15 matrix without fail-fast, weekly
+  scheduled run and manual trigger; style, manifest, coverage and docs
+  checked in a separate job. Read the Docs moved to Ubuntu 24.04 and
+  Python 3.12 with unpinned documentation dependencies.
+- Releases are published to PyPI by GitHub Actions with Trusted
+  Publishing (no API tokens); manual runs publish to TestPyPI.
+- ``make_df``: avoid ``inplace=True`` in ``set_index`` (deprecated in
+  pandas 3.1, to be removed in pandas 4).
+Version 0.1.1
+-------------
+- Fix ``read_df`` with pandas >= 2.0: column-name normalization replaced
+  every character with ``_`` (regex ``"."`` matched any character).
+- Fix spurious ``ChainedAssignmentError`` warning in ``CellData.__setitem__``
+  under pandas copy-on-write.
+- Add regression test for column-name normalization.

pycellid-0.2.0/MANIFEST.in ADDED Viewed

@@ -0,0 +1,5 @@
+include LICENSE
+include README.md
+include CHANGELOG.rst
+include pyproject.toml
+recursive-include pycellid *.py

{pycellid-0.1/pycellid.egg-info → pycellid-0.2.0}/PKG-INFO RENAMED Viewed

@@ -1,34 +1,46 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pycellid
-Version: 0.1
-Summary: Functions to analyze single-cell
-Home-page: https://github.com/pyCellID/pyCellID
-Author: Clemente, José
-Author-email: clemente.jac@gmail.com
-License: The MIT License
+Version: 0.2.0
+Summary: Functions to analyze Cell-ID single-cell cytometry data
+Author: Juan David Ferreira, Víctor San Martín
+Author-email: "José A. Clemente" <clemente.jac@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/pyCellID/pyCellID
+Project-URL: Documentation, https://pycellid.readthedocs.io
+Project-URL: Issues, https://github.com/pyCellID/pyCellID/issues
+Project-URL: Changelog, https://github.com/pyCellID/pyCellID/blob/main/CHANGELOG.rst
 Keywords: pycellid,cytometry,microscopy,cellid,vcellid
-Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Education
 Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3.15
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >= 3.8
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: attrs>=22.2
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2.0
+Dynamic: license-file
 ![logo](https://raw.githubusercontent.com/pyCellID/pyCellID/clementejose/docs/logo/PycellID_logo.jpg)
 # PyCellID
-[![Build status](https://github.com/pyCellID/pyCellID/actions/workflows/CI.yml/badge.svg)](https://github.com/pyCellID/pyCellID/actions)
+[![Build status](https://github.com/pyCellID/pyCellID/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/pyCellID/pyCellID/actions/workflows/CI.yml)
+[![PyPI](https://img.shields.io/pypi/v/pycellid)](https://pypi.org/project/pycellid/)
 [![codecov](https://codecov.io/gh/pyCellID/pyCellID/branch/main/graph/badge.svg?token=SXFRA6KCLV)](https://codecov.io/gh/pyCellID/pyCellID)
 [![Documentation Status](https://readthedocs.org/projects/pycellid/badge/?version=latest)](https://pycellid.readthedocs.io/en/latest/?badge=latest)
 [![issues](https://img.shields.io/github/issues/pyCellID/pyCellID)](https://img.shields.io/github/issues/pyCellID/pyCellID)
@@ -48,14 +60,14 @@ We hope to integrate tools for image segmentation in future releases. In that wa
 ## Requirements
-Python 3.8+
+Python 3.11+
 ## Dependecies for this project.
-- [attrs(>=21.1.0)](https://www.attrs.org/en/stable/) for building the backend.
-- [matplotlib(>=3.4.0)](https://matplotlib.org/) for plots management
-- [pandas(>=1.3.0)](https://pandas.pydata.org/) for panel and dashboard management.
-- [numpy(>=1.21.0)](https://numpy.org/) for numerical management.
+- [attrs(>=22.2)](https://www.attrs.org/en/stable/) for building the backend.
+- [matplotlib(>=3.7)](https://matplotlib.org/) for plots management
+- [pandas(>=2.0)](https://pandas.pydata.org/) for panel and dashboard management.
+- [numpy(>=1.24)](https://numpy.org/) for numerical management.
 ## Installation
@@ -74,8 +86,8 @@ For development, clone the [official github repository](https://github.com/pyCel
     $ cd pyCellID
     $ python3 -m venv venv
     $ source venv/bin/activate
-    $ pip install -e .
-    $ pip install -r requirements/dev.txt
+    $ pip install --upgrade pip
+    $ pip install -e . --group dev
 ```
 Run the tests with pytest:
@@ -125,5 +137,3 @@ We have got inspiration from [rcell and rcell2](https://github.com/darksideofthe
 This project is licensed under the MIT License (see the
 [LICENSE](https://github.com/pyCellID/pyCellID/blob/main/LICENSE) file for details).

{pycellid-0.1 → pycellid-0.2.0}/README.md RENAMED Viewed

@@ -2,7 +2,8 @@
 # PyCellID
-[![Build status](https://github.com/pyCellID/pyCellID/actions/workflows/CI.yml/badge.svg)](https://github.com/pyCellID/pyCellID/actions)
+[![Build status](https://github.com/pyCellID/pyCellID/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/pyCellID/pyCellID/actions/workflows/CI.yml)
+[![PyPI](https://img.shields.io/pypi/v/pycellid)](https://pypi.org/project/pycellid/)
 [![codecov](https://codecov.io/gh/pyCellID/pyCellID/branch/main/graph/badge.svg?token=SXFRA6KCLV)](https://codecov.io/gh/pyCellID/pyCellID)
 [![Documentation Status](https://readthedocs.org/projects/pycellid/badge/?version=latest)](https://pycellid.readthedocs.io/en/latest/?badge=latest)
 [![issues](https://img.shields.io/github/issues/pyCellID/pyCellID)](https://img.shields.io/github/issues/pyCellID/pyCellID)
@@ -22,14 +23,14 @@ We hope to integrate tools for image segmentation in future releases. In that wa
 ## Requirements
-Python 3.8+
+Python 3.11+
 ## Dependecies for this project.
-- [attrs(>=21.1.0)](https://www.attrs.org/en/stable/) for building the backend.
-- [matplotlib(>=3.4.0)](https://matplotlib.org/) for plots management
-- [pandas(>=1.3.0)](https://pandas.pydata.org/) for panel and dashboard management.
-- [numpy(>=1.21.0)](https://numpy.org/) for numerical management.
+- [attrs(>=22.2)](https://www.attrs.org/en/stable/) for building the backend.
+- [matplotlib(>=3.7)](https://matplotlib.org/) for plots management
+- [pandas(>=2.0)](https://pandas.pydata.org/) for panel and dashboard management.
+- [numpy(>=1.24)](https://numpy.org/) for numerical management.
 ## Installation
@@ -48,8 +49,8 @@ For development, clone the [official github repository](https://github.com/pyCel
     $ cd pyCellID
     $ python3 -m venv venv
     $ source venv/bin/activate
-    $ pip install -e .
-    $ pip install -r requirements/dev.txt
+    $ pip install --upgrade pip
+    $ pip install -e . --group dev
 ```
 Run the tests with pytest:

{pycellid-0.1 → pycellid-0.2.0}/pycellid/__init__.py RENAMED Viewed

@@ -25,7 +25,7 @@ An extension that analyze Cell-ID single-cell.
 # META
 # =============================================================================
-__version__ = "0.1"
+__version__ = "0.2.0"
 # =============================================================================
 # IMPORTS

{pycellid-0.1 → pycellid-0.2.0}/pycellid/core.py RENAMED Viewed

@@ -182,7 +182,7 @@ class CellData(object):
     def __setitem__(self, idx, values):
         """Call to implement assignment to ``self[key]``."""
-        return self._df.__setitem__(idx, values)
+        self._df[idx] = values
     def __iter__(self):
         """Call when an iterator is required for a container.

{pycellid-0.1 → pycellid-0.2.0}/pycellid/io.py RENAMED Viewed

@@ -69,7 +69,7 @@ def read_df(path_file):
     # Remove spaces in headers ' x.pos ' produced from cellid
     df.columns = df.columns.str.strip()
     # Change name delimiter "."" to "_"
-    df.columns = df.columns.str.replace(".", "_", regex=True)
+    df.columns = df.columns.str.replace(".", "_", regex=False)
     return df
@@ -161,7 +161,7 @@ def _make_cols_chan(df, df_map):
     # Remove redundant values from CellID.
     df_morf = df[df.flag == 0][morf]
-    df_morf.set_index(["ucid", "t_frame"], inplace=True)
+    df_morf = df_morf.set_index(["ucid", "t_frame"])
     # Merge df_flag y df_morf
     df = pd.merge(df_morf, df_flag, on=["ucid", "t_frame"], how="outer")

{pycellid-0.1 → pycellid-0.2.0/pycellid.egg-info}/PKG-INFO RENAMED Viewed

@@ -1,34 +1,46 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pycellid
-Version: 0.1
-Summary: Functions to analyze single-cell
-Home-page: https://github.com/pyCellID/pyCellID
-Author: Clemente, José
-Author-email: clemente.jac@gmail.com
-License: The MIT License
+Version: 0.2.0
+Summary: Functions to analyze Cell-ID single-cell cytometry data
+Author: Juan David Ferreira, Víctor San Martín
+Author-email: "José A. Clemente" <clemente.jac@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/pyCellID/pyCellID
+Project-URL: Documentation, https://pycellid.readthedocs.io
+Project-URL: Issues, https://github.com/pyCellID/pyCellID/issues
+Project-URL: Changelog, https://github.com/pyCellID/pyCellID/blob/main/CHANGELOG.rst
 Keywords: pycellid,cytometry,microscopy,cellid,vcellid
-Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Education
 Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3.15
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >= 3.8
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: attrs>=22.2
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2.0
+Dynamic: license-file
 ![logo](https://raw.githubusercontent.com/pyCellID/pyCellID/clementejose/docs/logo/PycellID_logo.jpg)
 # PyCellID
-[![Build status](https://github.com/pyCellID/pyCellID/actions/workflows/CI.yml/badge.svg)](https://github.com/pyCellID/pyCellID/actions)
+[![Build status](https://github.com/pyCellID/pyCellID/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/pyCellID/pyCellID/actions/workflows/CI.yml)
+[![PyPI](https://img.shields.io/pypi/v/pycellid)](https://pypi.org/project/pycellid/)
 [![codecov](https://codecov.io/gh/pyCellID/pyCellID/branch/main/graph/badge.svg?token=SXFRA6KCLV)](https://codecov.io/gh/pyCellID/pyCellID)
 [![Documentation Status](https://readthedocs.org/projects/pycellid/badge/?version=latest)](https://pycellid.readthedocs.io/en/latest/?badge=latest)
 [![issues](https://img.shields.io/github/issues/pyCellID/pyCellID)](https://img.shields.io/github/issues/pyCellID/pyCellID)
@@ -48,14 +60,14 @@ We hope to integrate tools for image segmentation in future releases. In that wa
 ## Requirements
-Python 3.8+
+Python 3.11+
 ## Dependecies for this project.
-- [attrs(>=21.1.0)](https://www.attrs.org/en/stable/) for building the backend.
-- [matplotlib(>=3.4.0)](https://matplotlib.org/) for plots management
-- [pandas(>=1.3.0)](https://pandas.pydata.org/) for panel and dashboard management.
-- [numpy(>=1.21.0)](https://numpy.org/) for numerical management.
+- [attrs(>=22.2)](https://www.attrs.org/en/stable/) for building the backend.
+- [matplotlib(>=3.7)](https://matplotlib.org/) for plots management
+- [pandas(>=2.0)](https://pandas.pydata.org/) for panel and dashboard management.
+- [numpy(>=1.24)](https://numpy.org/) for numerical management.
 ## Installation
@@ -74,8 +86,8 @@ For development, clone the [official github repository](https://github.com/pyCel
     $ cd pyCellID
     $ python3 -m venv venv
     $ source venv/bin/activate
-    $ pip install -e .
-    $ pip install -r requirements/dev.txt
+    $ pip install --upgrade pip
+    $ pip install -e . --group dev
 ```
 Run the tests with pytest:
@@ -125,5 +137,3 @@ We have got inspiration from [rcell and rcell2](https://github.com/darksideofthe
 This project is licensed under the MIT License (see the
 [LICENSE](https://github.com/pyCellID/pyCellID/blob/main/LICENSE) file for details).

{pycellid-0.1 → pycellid-0.2.0}/pycellid.egg-info/SOURCES.txt RENAMED Viewed

@@ -2,7 +2,7 @@ CHANGELOG.rst
 LICENSE
 MANIFEST.in
 README.md
-setup.py
+pyproject.toml
 pycellid/__init__.py
 pycellid/core.py
 pycellid/images.py
@@ -11,4 +11,7 @@ pycellid.egg-info/PKG-INFO
 pycellid.egg-info/SOURCES.txt
 pycellid.egg-info/dependency_links.txt
 pycellid.egg-info/requires.txt
-pycellid.egg-info/top_level.txt
+pycellid.egg-info/top_level.txt
+tests/test_core.py
+tests/test_images.py
+tests/test_io.py

pycellid-0.2.0/pycellid.egg-info/requires.txt ADDED Viewed

@@ -0,0 +1,4 @@
+attrs>=22.2
+matplotlib>=3.7
+numpy>=1.24
+pandas>=2.0

pycellid-0.2.0/pyproject.toml ADDED Viewed

@@ -0,0 +1,108 @@
+# =============================================================================
+# BUILD SYSTEM: qué herramienta construye el paquete
+# =============================================================================
+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+# =============================================================================
+# PROJECT: metadata del paquete (PEP 621)
+# =============================================================================
+[project]
+name = "pycellid"
+dynamic = ["version"]
+description = "Functions to analyze Cell-ID single-cell cytometry data"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+requires-python = ">=3.11"
+authors = [
+    { name = "José A. Clemente", email = "clemente.jac@gmail.com" },
+    { name = "Juan David Ferreira" },
+    { name = "Víctor San Martín" },
+]
+keywords = ["pycellid", "cytometry", "microscopy", "cellid", "vcellid"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: 3.15",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+dependencies = [
+    "attrs>=22.2",
+    "matplotlib>=3.7",
+    "numpy>=1.24",
+    "pandas>=2.0",
+]
+[project.urls]
+Homepage = "https://github.com/pyCellID/pyCellID"
+Documentation = "https://pycellid.readthedocs.io"
+Issues = "https://github.com/pyCellID/pyCellID/issues"
+Changelog = "https://github.com/pyCellID/pyCellID/blob/main/CHANGELOG.rst"
+# =============================================================================
+# DEPENDENCY GROUPS: dependencias para desarrollar (PEP 735)
+# No se publican en PyPI ni las instala el usuario final.
+# =============================================================================
+[dependency-groups]
+test = ["pytest>=8", "pytest-cov"]
+style = ["flake8", "flake8-import-order", "flake8-builtins", "pep8-naming"]
+docstyle = ["pydocstyle[toml]"]
+dev = [
+    { include-group = "test" },
+    { include-group = "style" },
+    { include-group = "docstyle" },
+    "check-manifest",
+    "build",
+    "twine",
+    "tox>=4.22",
+]
+# =============================================================================
+# SETUPTOOLS: configuración específica de la herramienta de build
+# =============================================================================
+[tool.setuptools]
+packages = ["pycellid"]
+[tool.setuptools.dynamic]
+version = { attr = "pycellid.__version__" }
+# =============================================================================
+# OTRAS HERRAMIENTAS
+# =============================================================================
+[tool.black]
+line-length = 79
+target-version = ["py311"]
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+[tool.check-manifest]
+# Archivos versionados en git que a propósito NO van en el sdist
+ignore = [
+    ".github/**",
+    ".gitignore",
+    ".readthedocs.yaml",
+    "docs/**",
+    "samples_cellid/**",
+    "tests/**",
+    "tox.ini",
+]

pycellid 0.1__tar.gz → 0.2.0__tar.gz

pycellid 0.1tar.gz → 0.2.0tar.gz