Update dependencies and Python version>=3.10 (#57)

* Update dependencies and Python version>=3.10

* Add GH workflows

* remove travis configuration

* Remove unused badges and bump up version

* add RTD config

* Populate yml

* Update rtd yaml path

* UPdate .readthedocs

* another try

* Update makefile

* correct conf.py path

* Use RTD theme

.github/workflows/full_tests.yml

@@ -0,0 +1,27 @@
+name: Test on Ubuntu
+
+on:
+  pull_request:
+      branches: [master]
+      types: [synchronize, opened, reopened]
+
+
+jobs:
+  build-and-test:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .
+        pip install pytest
+    - name: Pytest
+      run: |
+        pytest -v

.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,29 @@
+name: Release to PyPI
+
+on:
+  push:
+    tags:
+       - '*'
+jobs:
+  release:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - name: Install Tools
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine build
+    - name: Package and Upload
+      env:
+        STACKMANAGER_VERSION: ${{ github.event.release.tag_name }}
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: |
+        python -m build --sdist --wheel
+        twine upload dist/*

.readthedocs.yaml

@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+    - requirements: docs/requirements.txt

README.md

@@ -1,8 +1,5 @@
-[![Build Status](https://travis-ci.org/CINPLA/expipe.svg?branch=dev)](https://travis-ci.org/CINPLA/expipe)
-[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
+[![Build Status](https://github.com/CINPLA/expipe/actions/workflows/full_tests.yml/badge.svg)](https://github.com/CINPLA/expipe/actions/workflows/full_tests.yml/badge.svg)[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
 [![PyPI version](https://badge.fury.io/py/expipe.svg)](https://badge.fury.io/py/expipe)
-[![Anaconda-Server Badge](https://anaconda.org/cinpla/expipe/badges/installer/conda.svg)](https://conda.anaconda.org/cinpla/expipe)
-[![codecov](https://codecov.io/gh/CINPLA/expipe/branch/dev/graph/badge.svg)](https://codecov.io/gh/CINPLA/expipe)
 
 # Expipe
 

docs/Makefile

@@ -1,10 +1,10 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = expipe
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build
 

docs/conf.py

@@ -21,19 +21,16 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
-import os
 import re
 import expipe
 
-on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
-if not on_rtd:  # only import and set the theme if we're building docs locally
-    try:
-        import sphinx_rtd_theme
-        html_theme = "sphinx_rtd_theme"
-        html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
-    except ImportError:
-        print("RTD theme not installed, using default")
-        pass
+try:
+    import sphinx_rtd_theme
+    html_theme = "sphinx_rtd_theme"
+    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+except ImportError:
+    print("RTD theme not installed, using default")
+    pass
 
 # -- General configuration ------------------------------------------------
 

docs/requirements.txt

@@ -0,0 +1,2 @@
+sphinx
+sphinx_rtd_theme

environment.yml

@@ -1,6 +1,6 @@
-name: expipe
+name: expipe-test
 dependencies:
-  - python=3.5
+  - python=3.10
   - numpy
   - matplotlib
   - scipy

expipe/backends/filesystem.py

@@ -54,7 +54,7 @@ def convert_quantities(value):
         result = value.tolist()
     elif isinstance(value, np.integer):
         result = int(value)
-    elif isinstance(value, np.float):
+    elif isinstance(value, float):
         result = float(value)
     else:
         # try if dictionary like objects can be converted if not return the
@@ -76,17 +76,16 @@ def convert_quantities(value):
 def yaml_dump(f, data):
     assert f.suffix == '.yaml'
     with f.open("w", encoding="utf-8") as fh:
-        yaml.dump(
+        yaml_ = yaml.YAML(typ='safe', pure=True)
+        yaml_.dump(
             convert_quantities(data), fh,
-            default_flow_style=False,
-            allow_unicode=True,
-            Dumper=yaml.RoundTripDumper
         )
 
 
 def yaml_load(path):
     with path.open('r', encoding='utf-8') as f:
-        result = yaml.load(f, Loader=yaml.Loader)
+        yaml_ = yaml.YAML(typ='safe', pure=True)
+        result = yaml_.load(f)
     return convert_back_quantities(result)
 
 

expipe/config.py

@@ -35,19 +35,19 @@ def _load_config(path):
         result = {}
     else:
         with path.open('r') as f:
-            result = yaml.safe_load(f)
+            yaml_ = yaml.YAML(typ='safe', pure=True)
+            result = yaml_.load(f)
     return result
 
 
 def _dump_config(path, contents):
     assert path.suffix == '.yaml'
     path.parent.mkdir(exist_ok=True, parents=True)
     with path.open("w", encoding="utf-8") as f:
-        yaml.dump(
+        yaml_ = yaml.YAML(typ='safe', pure=True)
+        yaml_.dump(
             contents, f,
-            default_flow_style=False,
-            allow_unicode=True,
-            Dumper=yaml.RoundTripDumper)
+        )
 
 
 def _load_config_by_name(config=None):

expipe/core.py

@@ -406,6 +406,7 @@ def type(self, value):
             raise TypeError('Expected "str" got "' + str(type(value)) + '"')
         self._backend.attributes.set('type', value)
 
+
     @property
     def datetime(self):
         dtime = self._backend.attributes.get('datetime')
@@ -671,11 +672,13 @@ def delete_project(self, name, remove_all_children=None):
 # Entry API
 def get_project(path, name=None):
     import expipe.backends.filesystem
+    from expipe.config import settings
+
     path = pathlib.Path(path).absolute()
 
     name = name or path.stem
 
-    global_config = config.settings.copy()
+    global_config = settings.copy()
 
     local_config_path = path / "expipe.yaml"
     if not local_config_path.exists():
@@ -723,9 +726,13 @@ def create_project(path, name=None, init=False):
         "type": "project",
         "project": name
     }
+    print(local_config)
 
     with local_config_path.open('w') as f:
-        yaml.dump(local_config, f)
+        yaml_ = yaml.YAML(typ='safe', pure=True)
+        yaml_.dump(
+            local_config, f,
+        )
 
     return get_project(path)
 

expipe/version.py

@@ -1 +1 @@
-version = '0.5.1'
+version = '0.6.0'

requirements.txt

@@ -1,6 +1,6 @@
-numpy
-ruamel.yaml
-quantities
-pandas
-ipywidgets
-click
+numpy>=1.25
+ruamel.yaml>=0.18.5
+quantities>=0.14.1
+pandas>=2.1.2
+ipywidgets>=8.1.1
+click>=8.1.7

setup.py

@@ -39,4 +39,5 @@
                    'Natural Language :: English',
                    'Programming Language :: Python :: 3',
                    'Topic :: Scientific/Engineering'],
+      python_requires='>=3.9',
       )