Skip to content

Commit d5add57

Browse files
authored
Merge pull request #5 from ACCESS-NRI/lindsey/4-requirements-for-perturbic
Update perturbIC.py
2 parents 435bea4 + e8a0be2 commit d5add57

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

78 files changed

+1674
-16877
lines changed

.coverage

52 KB
Binary file not shown.

.coveragerc

+9
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,9 @@
1+
[run]
2+
branch = True
3+
4+
# skip coverage testing for external source files
5+
omit = src/umfile_utils/_version.py
6+
7+
[html]
8+
title = Coverage report: umfile_utils
9+
directory = coverage_html
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,45 @@
1+
name: CI
2+
3+
on:
4+
push:
5+
branches: main
6+
pull_request:
7+
branches: main
8+
workflow_dispatch:
9+
10+
jobs:
11+
12+
test:
13+
runs-on: ubuntu-latest
14+
strategy:
15+
fail-fast: false
16+
matrix:
17+
python-version: ["3.10", "3.11", "3.12"]
18+
19+
steps:
20+
- name: Checkout Repository
21+
uses: actions/checkout@v4
22+
23+
- name: Setup conda environment
24+
uses: conda-incubator/setup-miniconda@v3
25+
with:
26+
miniconda-version: "latest"
27+
python-version: ${{ matrix.python-version }}
28+
environment-file: environment-dev.yml
29+
auto-activate-base: false
30+
activate-environment: umfile-utils-dev
31+
auto-update-conda: false
32+
show-channel-urls: true
33+
34+
- name: Install source
35+
shell: bash -l {0}
36+
run: python -m pip install --no-deps --no-build-isolation -e .
37+
38+
- name: List installed packages
39+
shell: bash -l {0}
40+
run: conda list
41+
42+
- name: Run tests
43+
shell: bash -l {0}
44+
run: python -m pytest --cov=src --cov-report=html -s tests
45+

.gitignore

+12
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
**/__pycache__/
2+
*.pyc
3+
.hypothesis/
4+
.*_cache/
5+
.vscode/
6+
.DS_Store
7+
.idea
8+
.coverage
9+
*~
10+
*.egg-info
11+
coverage_html
12+
*.code-workspace

LICENSE

+201
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,201 @@
1+
Apache License
2+
Version 2.0, January 2004
3+
http://www.apache.org/licenses/
4+
5+
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
6+
7+
1. Definitions.
8+
9+
"License" shall mean the terms and conditions for use, reproduction,
10+
and distribution as defined by Sections 1 through 9 of this document.
11+
12+
"Licensor" shall mean the copyright owner or entity authorized by
13+
the copyright owner that is granting the License.
14+
15+
"Legal Entity" shall mean the union of the acting entity and all
16+
other entities that control, are controlled by, or are under common
17+
control with that entity. For the purposes of this definition,
18+
"control" means (i) the power, direct or indirect, to cause the
19+
direction or management of such entity, whether by contract or
20+
otherwise, or (ii) ownership of fifty percent (50%) or more of the
21+
outstanding shares, or (iii) beneficial ownership of such entity.
22+
23+
"You" (or "Your") shall mean an individual or Legal Entity
24+
exercising permissions granted by this License.
25+
26+
"Source" form shall mean the preferred form for making modifications,
27+
including but not limited to software source code, documentation
28+
source, and configuration files.
29+
30+
"Object" form shall mean any form resulting from mechanical
31+
transformation or translation of a Source form, including but
32+
not limited to compiled object code, generated documentation,
33+
and conversions to other media types.
34+
35+
"Work" shall mean the work of authorship, whether in Source or
36+
Object form, made available under the License, as indicated by a
37+
copyright notice that is included in or attached to the work
38+
(an example is provided in the Appendix below).
39+
40+
"Derivative Works" shall mean any work, whether in Source or Object
41+
form, that is based on (or derived from) the Work and for which the
42+
editorial revisions, annotations, elaborations, or other modifications
43+
represent, as a whole, an original work of authorship. For the purposes
44+
of this License, Derivative Works shall not include works that remain
45+
separable from, or merely link (or bind by name) to the interfaces of,
46+
the Work and Derivative Works thereof.
47+
48+
"Contribution" shall mean any work of authorship, including
49+
the original version of the Work and any modifications or additions
50+
to that Work or Derivative Works thereof, that is intentionally
51+
submitted to Licensor for inclusion in the Work by the copyright owner
52+
or by an individual or Legal Entity authorized to submit on behalf of
53+
the copyright owner. For the purposes of this definition, "submitted"
54+
means any form of electronic, verbal, or written communication sent
55+
to the Licensor or its representatives, including but not limited to
56+
communication on electronic mailing lists, source code control systems,
57+
and issue tracking systems that are managed by, or on behalf of, the
58+
Licensor for the purpose of discussing and improving the Work, but
59+
excluding communication that is conspicuously marked or otherwise
60+
designated in writing by the copyright owner as "Not a Contribution."
61+
62+
"Contributor" shall mean Licensor and any individual or Legal Entity
63+
on behalf of whom a Contribution has been received by Licensor and
64+
subsequently incorporated within the Work.
65+
66+
2. Grant of Copyright License. Subject to the terms and conditions of
67+
this License, each Contributor hereby grants to You a perpetual,
68+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
69+
copyright license to reproduce, prepare Derivative Works of,
70+
publicly display, publicly perform, sublicense, and distribute the
71+
Work and such Derivative Works in Source or Object form.
72+
73+
3. Grant of Patent License. Subject to the terms and conditions of
74+
this License, each Contributor hereby grants to You a perpetual,
75+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
76+
(except as stated in this section) patent license to make, have made,
77+
use, offer to sell, sell, import, and otherwise transfer the Work,
78+
where such license applies only to those patent claims licensable
79+
by such Contributor that are necessarily infringed by their
80+
Contribution(s) alone or by combination of their Contribution(s)
81+
with the Work to which such Contribution(s) was submitted. If You
82+
institute patent litigation against any entity (including a
83+
cross-claim or counterclaim in a lawsuit) alleging that the Work
84+
or a Contribution incorporated within the Work constitutes direct
85+
or contributory patent infringement, then any patent licenses
86+
granted to You under this License for that Work shall terminate
87+
as of the date such litigation is filed.
88+
89+
4. Redistribution. You may reproduce and distribute copies of the
90+
Work or Derivative Works thereof in any medium, with or without
91+
modifications, and in Source or Object form, provided that You
92+
meet the following conditions:
93+
94+
(a) You must give any other recipients of the Work or
95+
Derivative Works a copy of this License; and
96+
97+
(b) You must cause any modified files to carry prominent notices
98+
stating that You changed the files; and
99+
100+
(c) You must retain, in the Source form of any Derivative Works
101+
that You distribute, all copyright, patent, trademark, and
102+
attribution notices from the Source form of the Work,
103+
excluding those notices that do not pertain to any part of
104+
the Derivative Works; and
105+
106+
(d) If the Work includes a "NOTICE" text file as part of its
107+
distribution, then any Derivative Works that You distribute must
108+
include a readable copy of the attribution notices contained
109+
within such NOTICE file, excluding those notices that do not
110+
pertain to any part of the Derivative Works, in at least one
111+
of the following places: within a NOTICE text file distributed
112+
as part of the Derivative Works; within the Source form or
113+
documentation, if provided along with the Derivative Works; or,
114+
within a display generated by the Derivative Works, if and
115+
wherever such third-party notices normally appear. The contents
116+
of the NOTICE file are for informational purposes only and
117+
do not modify the License. You may add Your own attribution
118+
notices within Derivative Works that You distribute, alongside
119+
or as an addendum to the NOTICE text from the Work, provided
120+
that such additional attribution notices cannot be construed
121+
as modifying the License.
122+
123+
You may add Your own copyright statement to Your modifications and
124+
may provide additional or different license terms and conditions
125+
for use, reproduction, or distribution of Your modifications, or
126+
for any such Derivative Works as a whole, provided Your use,
127+
reproduction, and distribution of the Work otherwise complies with
128+
the conditions stated in this License.
129+
130+
5. Submission of Contributions. Unless You explicitly state otherwise,
131+
any Contribution intentionally submitted for inclusion in the Work
132+
by You to the Licensor shall be under the terms and conditions of
133+
this License, without any additional terms or conditions.
134+
Notwithstanding the above, nothing herein shall supersede or modify
135+
the terms of any separate license agreement you may have executed
136+
with Licensor regarding such Contributions.
137+
138+
6. Trademarks. This License does not grant permission to use the trade
139+
names, trademarks, service marks, or product names of the Licensor,
140+
except as required for reasonable and customary use in describing the
141+
origin of the Work and reproducing the content of the NOTICE file.
142+
143+
7. Disclaimer of Warranty. Unless required by applicable law or
144+
agreed to in writing, Licensor provides the Work (and each
145+
Contributor provides its Contributions) on an "AS IS" BASIS,
146+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
147+
implied, including, without limitation, any warranties or conditions
148+
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
149+
PARTICULAR PURPOSE. You are solely responsible for determining the
150+
appropriateness of using or redistributing the Work and assume any
151+
risks associated with Your exercise of permissions under this License.
152+
153+
8. Limitation of Liability. In no event and under no legal theory,
154+
whether in tort (including negligence), contract, or otherwise,
155+
unless required by applicable law (such as deliberate and grossly
156+
negligent acts) or agreed to in writing, shall any Contributor be
157+
liable to You for damages, including any direct, indirect, special,
158+
incidental, or consequential damages of any character arising as a
159+
result of this License or out of the use or inability to use the
160+
Work (including but not limited to damages for loss of goodwill,
161+
work stoppage, computer failure or malfunction, or any and all
162+
other commercial damages or losses), even if such Contributor
163+
has been advised of the possibility of such damages.
164+
165+
9. Accepting Warranty or Additional Liability. While redistributing
166+
the Work or Derivative Works thereof, You may choose to offer,
167+
and charge a fee for, acceptance of support, warranty, indemnity,
168+
or other liability obligations and/or rights consistent with this
169+
License. However, in accepting such obligations, You may act only
170+
on Your own behalf and on Your sole responsibility, not on behalf
171+
of any other Contributor, and only if You agree to indemnify,
172+
defend, and hold each Contributor harmless for any liability
173+
incurred by, or claims asserted against, such Contributor by reason
174+
of your accepting any such warranty or additional liability.
175+
176+
END OF TERMS AND CONDITIONS
177+
178+
APPENDIX: How to apply the Apache License to your work.
179+
180+
To apply the Apache License to your work, attach the following
181+
boilerplate notice, with the fields enclosed by brackets "[]"
182+
replaced with your own identifying information. (Don't include
183+
the brackets!) The text should be enclosed in the appropriate
184+
comment syntax for the file format. We also recommend that a
185+
file or class name and description of purpose be included on the
186+
same "printed page" as the copyright notice for easier
187+
identification within third-party archives.
188+
189+
Copyright [yyyy] [name of copyright owner]
190+
191+
Licensed under the Apache License, Version 2.0 (the "License");
192+
you may not use this file except in compliance with the License.
193+
You may obtain a copy of the License at
194+
195+
http://www.apache.org/licenses/LICENSE-2.0
196+
197+
Unless required by applicable law or agreed to in writing, software
198+
distributed under the License is distributed on an "AS IS" BASIS,
199+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
200+
See the License for the specific language governing permissions and
201+
limitations under the License.

environment-dev.yml

+18
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,18 @@
1+
name: umfile-utils-dev
2+
channels:
3+
- accessnri
4+
- conda-forge
5+
- coecms
6+
- nodefaults
7+
dependencies:
8+
- python >=3.10
9+
- pytest
10+
- xarray
11+
- mule
12+
- numpy < 2
13+
- versioneer
14+
- hypothesis
15+
- ipykernel
16+
- pytest-cov
17+
- pip
18+

pyproject.toml

+43
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,43 @@
1+
[project]
2+
name = "umfile-utils"
3+
dynamic = ["version"]
4+
authors = [
5+
{name = "Martin Dix", email="[email protected]"},
6+
{name = "Lindsey Oberhelman", email="[email protected]"},
7+
{name = "Davide Marchegiani", email="[email protected]"},
8+
]
9+
description = "Collection of tools for UM fieldsfiles."
10+
license = { file = "LICENSE" }
11+
keywords = ["UM", "UM utilities", "UM fields files", "umfile_utils"]
12+
requires-python = ">=3.10"
13+
dependencies = [
14+
"mule",
15+
"numpy <2",
16+
"versioneer",
17+
]
18+
19+
[project.urls]
20+
Repository = "https://github.com/ACCESS-NRI/umfile_utils"
21+
22+
[build-system]
23+
build-backend = "setuptools.build_meta"
24+
requires = [
25+
"setuptools>64",
26+
"versioneer[toml]"
27+
]
28+
29+
[tool.setuptools.packages.find]
30+
where = ["src"]
31+
namespaces = false
32+
33+
[tool.versioneer]
34+
VCS = "git"
35+
style = "pep440"
36+
versionfile_source = "src/umfile_utils/_version.py"
37+
versionfile_build = "umfile_utils/_version.py"
38+
tag_prefix = ""
39+
parentdir_prefix = "umfile-utils-"
40+
41+
[tool.pytest.ini_options]
42+
pythonpath = "src"
43+
addopts = "--cov=src --cov-report=term-missing"

setup.py

+7
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,7 @@
1+
import versioneer
2+
from setuptools import setup
3+
4+
setup(
5+
version=versioneer.get_version(),
6+
cmdclass=versioneer.get_cmdclass(),
7+
)

0 commit comments

Comments
 (0)