1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
|
name: Tests
on:
pull_request:
push:
branches-ignore:
- 'dependabot/**'
- 'pre-commit-ci-update-config'
workflow_dispatch:
jobs:
run_test_site:
name: ${{ matrix.os }}-${{ matrix.os_version }}-py${{ matrix.PYTHON_VERSION }}${{ matrix.LABEL }}
runs-on: ${{ matrix.os }}-${{ matrix.os_version }}
timeout-minutes: 30
env:
MPLBACKEND: agg
strategy:
fail-fast: false
matrix:
os: [ubuntu, windows, macos]
os_version: [latest]
PYTHON_VERSION: ['3.9', '3.10']
LABEL: ['']
include:
# test oldest supported version of main dependencies on python 3.8
- os: ubuntu
os_version: latest
PYTHON_VERSION: '3.9'
# Set pillow and scikit-image version to be compatible with imageio and scipy
# align matplotlib dependency with hyperspy
DEPENDENCIES: matplotlib==3.6 numpy==1.20.0 tifffile==2022.7.28 dask[array]==2021.5.1 distributed==2021.5.1 numba==0.53 imageio==2.16 pillow==8.3.2 scikit-image==0.18.0 python-box==6.0.0
LABEL: '-oldest'
# test minimum requirement
- os: ubuntu
os_version: latest
PYTHON_VERSION: '3.10'
LABEL: '-minimum'
- os: ubuntu
os_version: latest
PYTHON_VERSION: '3.12'
LABEL: '-hyperspy-dev'
- os: ubuntu
os_version: latest
PYTHON_VERSION: '3.10'
LABEL: '-without-hyperspy'
- os: ubuntu
os_version: latest
PYTHON_VERSION: '3.9'
- os: ubuntu
os_version: latest
PYTHON_VERSION: '3.12'
- os: ubuntu
os_version: latest
PYTHON_VERSION: '3.13'
# can remove minimum dependencies when numba supports 3.13
LABEL: '-minimum'
- os: macos
os_version: latest
PYTHON_VERSION: '3.13'
# can remove minimum dependencies when numba supports 3.13
LABEL: '-minimum'
- os: windows
os_version: latest
PYTHON_VERSION: '3.13'
# can remove minimum dependencies when numba supports 3.13
LABEL: '-minimum'
- os: macos
os_version: '13'
PYTHON_VERSION: '3.12'
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: get repository name
shell: bash
run: echo "REPOSITORY_NAME=${GITHUB_REPOSITORY#*/}" >> $GITHUB_ENV
- name: Fetch tags upstream
if: ${{ github.repository_owner != 'hyperspy' }}
# Needs to fetch the tags from upstream to get the
# correct version with setuptools_scm
run: |
git remote add upstream https://github.com/hyperspy/${{ env.REPOSITORY_NAME }}.git
git fetch upstream --tags
- uses: actions/setup-python@v5
name: Install Python
with:
python-version: ${{ matrix.PYTHON_VERSION }}
cache: 'pip'
- name: Get the number of CPUs
id: cpus
run: |
import os, platform
num_cpus = os.cpu_count()
print(f"Number of CPU: {num_cpus}")
print(f"Architecture: {platform.machine()}")
output_file = os.environ["GITHUB_OUTPUT"]
with open(output_file, "a", encoding="utf-8") as output_stream:
output_stream.write(f"count={num_cpus}\n")
shell: python
- name: Set Environment Variable
shell: bash
# Set PIP_SELECTOR environment variable according to matrix.LABEL
run: |
if [[ -n "${{ matrix.LABEL }}" && "${{ matrix.LABEL }}" == *"minimum"* ]]; then
PIP_SELECTOR="[tests]"
else
PIP_SELECTOR="[all, tests]"
fi
echo "PIP_SELECTOR=${PIP_SELECTOR}" >> $GITHUB_ENV
- name: Display version
run: |
python --version
pip --version
- name: Install traits dev for python 3.13
if: ${{ matrix.PYTHON_VERSION == '3.13' }}
run: |
# traits release with python 3.13 pending
pip install git+https://github.com/enthought/traits.git
- name: Install hyperspy and exspy
if: ${{ ! contains(matrix.LABEL, 'without-hyperspy') && matrix.PYTHON_VERSION != '3.13'}}
run: |
pip install hyperspy exspy
- name: Install hyperspy and exspy (dev)
if: ${{ contains(matrix.LABEL, 'hyperspy-dev') }}
run: |
pip install git+https://github.com/hyperspy/hyperspy.git
pip install git+https://github.com/hyperspy/exspy.git
- name: Install hyperspy (python 3.13) and exspy (dev)
if: ${{ matrix.PYTHON_VERSION == '3.13' }}
run: |
# speed up installing scikit-image using pre-release with python 3.13 wheels
pip install scikit-image --pre
pip install git+https://github.com/ericpre/hyperspy.git@python313
pip install git+https://github.com/hyperspy/exspy.git
- name: Install python-mrcz dev
# for numpy 2.0 support for python >= 3.9
# https://github.com/em-MRCZ/python-mrcz/pull/15
if: ${{ ! contains(matrix.LABEL, 'oldest') && ! contains(matrix.LABEL, 'minimum') }}
run: |
pip install git+https://github.com/ericpre/python-mrcz.git@numpy2.0_and_deprecation_fixes
- name: Install
shell: bash
run: |
pip install --upgrade -e .'${{ env.PIP_SELECTOR }}'
- name: Uninstall pyUSID
# remove when pyUSID supports numpy 2
if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }}
run: |
pip uninstall -y pyUSID
- name: Install oldest supported version
if: contains(matrix.LABEL, 'oldest')
run: |
pip install ${{ matrix.DEPENDENCIES }}
- name: Install numpy 2.0
if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }}
run: |
pip install numpy>=2
- name: Pip list
run: |
pip list
- name: Run test suite
run: |
pytest --pyargs rsciio --reruns 3 -n ${{ steps.cpus.outputs.count }} --cov=. --cov-report=xml
- name: Upload coverage to Codecov
if: ${{ always() }}
uses: codecov/codecov-action@v5
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
|
