Merge pull request #164 from pescadores/2024-fixings

2024 fixings

.github/environment-ci.yml

@@ -0,0 +1,17 @@
+name: pescador-dev
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  # required
+  - pip
+  - six>=1.8
+  - pyzmq>=18.0
+  - decorator>=4.0
+
+  # optional, but required for testing
+  - pytest
+  - pytest-cov
+  - pytest-timeout>=1.2
+  - coverage
+  - scipy

.github/environment-minimal.yml

@@ -0,0 +1,17 @@
+name: pescador-dev
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  # required
+  - pip
+  - six~=1.8
+  - pyzmq~=18.0
+  - decorator~=4.0
+
+  # optional, but required for testing
+  - pytest
+  - pytest-cov
+  - pytest-timeout>=1.2
+  - coverage
+  - scipy

.github/workflows/ci.yml

@@ -0,0 +1,110 @@
+name: CI
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: True
+
+jobs:
+    test:
+        name: "Python ${{ matrix.python-version }} on ${{ matrix.os }}"
+        runs-on: ${{ matrix.os }}
+
+        strategy:
+            fail-fast: false
+            matrix:
+                include:
+                    - os: ubuntu-latest
+                      python-version: "3.7"
+                      envfile: ".github/environment-minimal.yml"
+                      channel-priority: "flexible"
+                      name: "Minimal dependencies"
+
+                    - os: ubuntu-latest
+                      python-version: "3.8"
+                      channel-priority: "strict"
+                      envfile: ".github/environment-ci.yml"
+
+                    - os: ubuntu-latest
+                      python-version: "3.9"
+                      channel-priority: "strict"
+                      envfile: ".github/environment-ci.yml"
+
+                    - os: ubuntu-latest
+                      python-version: "3.10"
+                      channel-priority: "strict"
+                      envfile: ".github/environment-ci.yml"
+
+                    - os: ubuntu-latest
+                      python-version: "3.11"
+                      channel-priority: "strict"
+                      envfile: ".github/environment-ci.yml"
+
+                    - os: macos-latest
+                      python-version: "3.11"
+                      channel-priority: "strict"
+                      envfile: ".github/environment-ci.yml"
+
+                    - os: windows-latest
+                      python-version: "3.11"
+                      channel-priority: "strict"
+                      envfile: ".github/environment-ci.yml"
+
+        steps:
+        - uses: actions/checkout@v3
+          with:
+            submodules: true
+
+        - name: Cache conda
+          uses: actions/cache@v3
+          env:
+            # Increase this value to reset cache if etc/example-environment.yml has not changed
+            CACHE_NUMBER: 0
+          with:
+            path: ~/conda_pkgs_dir
+            key: ${{ runner.os }}-${{ matrix.python-version }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles( matrix.envfile ) }}
+
+        - name: Install Conda environment
+          uses: conda-incubator/setup-miniconda@v2
+          with:
+            auto-update-conda: true
+            python-version: ${{ matrix.python-version }}
+            add-pip-as-python-dependency: true
+            auto-activate-base: false
+            activate-environment: test
+            channel-priority: ${{ matrix.channel-priority }}
+            environment-file: ${{ matrix.envfile }}
+            use-only-tar-bz2: false # IMPORTANT: This needs to be set for caching to work properly!
+
+        - name: Conda info
+          shell: bash -l {0}
+          run: |
+            conda info -a
+            conda list
+
+        - name: Install pescador
+          shell: bash -l {0}
+          run: python -m pip install --upgrade-strategy only-if-needed -e .[tests]
+
+        - name: Run pytest
+          shell: bash -l {0}
+          run: pytest
+
+        - name: Upload coverage to Codecov
+          uses: codecov/codecov-action@v3
+          with:
+            token: ${{ secrets.CODECOV_TOKEN }}
+            files: ./coverage.xml
+            directory: ./coverage/reports/
+            flags: unittests
+            env_vars: OS,PYTHON
+            name: codecov-umbrella
+            fail_ci_if_error: true
+            verbose: true

README.md

@@ -2,8 +2,8 @@ pescador
 ========
 [![PyPI](https://img.shields.io/pypi/v/pescador.svg)](https://pypi.python.org/pypi/pescador)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/pescador/badges/version.svg)](https://anaconda.org/conda-forge/pescador)
-[![Build Status](https://travis-ci.org/pescadores/pescador.svg?branch=master)](https://travis-ci.org/pescadores/pescador)
-[![Coverage Status](https://coveralls.io/repos/pescadores/pescador/badge.svg)](https://coveralls.io/r/pescadores/pescador)
+[![Build Status](https://github.com/pescadores/pescador/actions/workflows/ci.yml/badge.svg)](https://github.com/pescadores/pescador/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/pescadores/pescador/graph/badge.svg?token=aCgfizw6O5)](https://codecov.io/gh/pescadores/pescador)
 [![Documentation Status](https://readthedocs.org/projects/pescador/badge/?version=latest)](https://readthedocs.org/projects/pescador/?badge=latest)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.400700.svg)](https://doi.org/10.5281/zenodo.400700)
 

pescador/version.py

@@ -2,5 +2,5 @@
 # -*- coding: utf-8 -*-
 """Version info"""
 
-short_version = '2.1'
-version = '2.1.0'
+short_version = '3.0'
+version = '3.0.0-dev'

pescador/zmq_stream.py

@@ -16,34 +16,19 @@
 import multiprocessing as mp
 import zmq
 import numpy as np
-import six
-import sys
-import warnings
 
 try:
     import ujson as json
 except ImportError:
     import json
 
-try:
-    # joblib <= 0.9.4
-    from joblib.parallel import SafeFunction
-except ImportError:
-    # joblib >= 0.10.0
-    from joblib._parallel_backends import SafeFunction
-
 from .core import Streamer
 from .exceptions import DataError
 
 
 __all__ = ['ZMQStreamer']
 
 
-# A hack to support buffers in py3
-if six.PY3:
-    buffer = memoryview
-
-
 def zmq_send_data(socket, data, flags=0, copy=True, track=False):
     """Send data, e.g. {key: np.ndarray}, with metadata"""
 
@@ -82,12 +67,9 @@ def zmq_recv_data(socket, flags=0, copy=True, track=False):
         raise StopIteration
 
     for header, payload in zip(headers, msg[1:]):
-        data[header['key']] = np.frombuffer(buffer(payload),
+        data[header['key']] = np.frombuffer(memoryview(payload),
                                             dtype=header['dtype'])
         data[header['key']].shape = header['shape']
-        if six.PY2:
-            # Legacy python won't let us preserve alignment, skip this step
-            continue
         data[header['key']].flags['ALIGNED'] = header['aligned']
 
     return data
@@ -178,10 +160,6 @@ def iterate(self, max_iter=None):
         """
         context = zmq.Context()
 
-        if six.PY2:
-            warnings.warn('zmq_stream cannot preserve numpy array alignment '
-                          'in Python 2', RuntimeWarning)
-
         try:
             socket = context.socket(zmq.PAIR)
 
@@ -191,7 +169,7 @@ def iterate(self, max_iter=None):
                                               max_tries=self.max_tries)
             terminate = mp.Event()
 
-            worker = mp.Process(target=SafeFunction(zmq_worker),
+            worker = mp.Process(target=zmq_worker,
                                 args=[port, self.streamer, terminate],
                                 kwargs=dict(copy=self.copy,
                                             max_iter=max_iter))
@@ -206,13 +184,10 @@ def iterate(self, max_iter=None):
         except StopIteration:
             pass
 
-        except:
-            # pylint: disable-msg=W0702
-            six.reraise(*sys.exc_info())
-
         finally:
             terminate.set()
-            worker.join(self.timeout)
+            if worker.is_alive():
+                worker.join(self.timeout)
             if worker.is_alive():
                 worker.terminate()
             context.destroy()

setup.cfg

@@ -1,2 +1,46 @@
 [tool:pytest]
-addopts = --cov-report term-missing --cov pescador
+addopts = --cov-report term-missing --cov pescador --cov-report=xml
+
+[metadata]
+name = pescador
+version = attr: pescador.version.version
+description = Multiplex generators for incremental learning
+author = Pescador developers
+author_email = [email protected]
+url = https://github.com/pescadores/pescador
+download_url = https://github.com/pescadores/pescador/releases
+long_description  =  Multiplex generators for incremental learning
+license = ISC
+python_requires = ">=3.7"
+classifiers =
+    License :: OSI Approved :: ISC License (ISCL)
+    Programming Language :: Python
+    Development Status :: 3 - Alpha
+    Intended Audience :: Developers
+    Topic :: Multimedia :: Sound/Audio :: Analysis
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+
+[options]
+packages = find:
+keywords = machine learning
+install_requires =
+    six >= 1.8
+    pyzmq >= 18.0
+    numpy >= 1.9
+    decorator >= 4.0
+
+[options.extras_require]
+docs = 
+    numpydoc >= 0.6
+    sphinx-gallery >= 0.1.10
+tests = 
+    pytest
+    pytest-timeout>=1.2
+    pytest-cov
+    scipy
+