Skip to content

Commit 80a29e5

Browse files
FosowlFosowl
committed
gerge branch 'main' into dev
2 parents 2c4a3d4 + a753b3f commit 80a29e5

13 files changed

Lines changed: 427 additions & 1 deletion

File tree

‎.github/pull_request_template.md‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,10 @@
1+
## Contribution checklist
2+
3+
Please confirm the following before requesting review:
4+
5+
- [ ] I have read [`CONTRIBUTING.md`](/CONTRIBUTING.md), [`docs/licensing-notes.md`](/docs/licensing-notes.md), and the repository license information ([`LICENSE`](/LICENSE)) for this repository (Apache License 2.0).
6+
- [ ] I have read [`docs/cla-process.md`](/docs/cla-process.md) and understand the CLA workflow for contributions.
7+
- [ ] I confirm that I have the legal right to submit this contribution.
8+
- [ ] I have signed the required CLA, or I will complete the CLA process if requested.
9+
- [ ] If this is my first contribution, I understand that I may be asked to sign the CLA through the PR thread or status checks.
10+
- [ ] I am not knowingly submitting code or content under terms incompatible with Apache License 2.0.

‎.github/workflows/cla.yml‎

Lines changed: 29 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,29 @@
1+
name: CLA Check
2+
3+
on:
4+
pull_request_target:
5+
types: [opened, synchronize, closed]
6+
issue_comment:
7+
types: [created]
8+
9+
permissions:
10+
contents: write
11+
pull-requests: write
12+
statuses: write
13+
14+
jobs:
15+
cla_check:
16+
name: CLA Check
17+
if: github.event_name == 'pull_request_target' || (github.event_name == 'issue_comment' && github.event.issue.pull_request)
18+
runs-on: ubuntu-latest
19+
steps:
20+
- name: Run CLA Assistant Lite
21+
if: github.event_name == 'pull_request_target' || github.event.comment.body == 'recheck' || github.event.comment.body == 'I have read the CLA Document and I hereby sign the CLA'
22+
uses: contributor-assistant/github-action@v2.6.1
23+
env:
24+
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
25+
with:
26+
path-to-signatures: signatures/version1/cla.json
27+
path-to-document: https://github.com/${{ github.repository }}/blob/${{ github.event.repository.default_branch }}/CLA/INDIVIDUAL_CLA.md
28+
branch: ${{ github.event.repository.default_branch }}
29+
allowlist: dependabot[bot],github-actions[bot],renovate[bot]

‎.gitignore‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -234,7 +234,7 @@ vignettes/*.pdf
234234
.Renviron
235235

236236
# pkgdown site
237-
docs/
237+
#docs/
238238

239239
# translation temp files
240240
po/*~

‎CLA/EMPLOYER_AUTHORIZATION.md‎

Lines changed: 40 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,40 @@
1+
# Optional Employer / Institutional Authorization
2+
3+
> Template for repository governance. Confirm with CNRS counsel before production use.
4+
5+
Use this form only when a contributor is submitting material in the course of employment or under institutional intellectual-property rules.
6+
7+
Organization information:
8+
9+
- Organization: `[LEGAL ENTITY NAME]`
10+
- Authorized Signatory: `[NAME AND TITLE]`
11+
- Contact Email: `[ORGANIZATION CONTACT EMAIL]`
12+
- Address: `[REGISTERED ADDRESS]`
13+
- Date: `[DATE]`
14+
15+
Contributor(s) covered by this authorization:
16+
17+
| Full Name | Email | Team/Department |
18+
| --- | --- | --- |
19+
| `[NAME]` | `[EMAIL]` | `[TEAM]` |
20+
21+
Project:
22+
23+
- `Toolomics`, publicly distributed under the Apache License 2.0
24+
- Maintainer contact for contribution-governance questions: `dr20.spv@listes.cnrs.fr`
25+
26+
By signing this authorization, the organization confirms that:
27+
28+
1. It has sufficient authority to allow the listed contributor(s) to submit contributions to `Toolomics`.
29+
2. It permits those contributions to be intentionally submitted for inclusion in `Toolomics` under the Apache License 2.0.
30+
3. To the best of its knowledge, those contributions are not knowingly subject to terms incompatible with the Apache License 2.0.
31+
4. Except for the rights granted through submission under the Apache License 2.0, the organization and/or contributors retain ownership of their copyrights.
32+
5. This authorization does not require copyright assignment and is not intended to create a second licensing track.
33+
6. Nothing in this authorization obligates the project maintainers to accept or use any contribution.
34+
35+
Authorized signature:
36+
37+
- Organization: `[LEGAL ENTITY NAME]`
38+
- Name/Title: `[AUTHORIZED SIGNATORY]`
39+
- Signature: `[SIGNATURE]`
40+
- Date: `[DATE]`

‎CLA/INDIVIDUAL_CLA.md‎

Lines changed: 35 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,35 @@
1+
# Short Individual Contributor Agreement (CLA)
2+
3+
> Template for repository governance. Confirm with CNRS counsel before production use.
4+
5+
This short agreement is intended for non-trivial external contributions to `Toolomics`.
6+
7+
Contributor information:
8+
9+
- Name: `[FULL LEGAL NAME]`
10+
- Email: `[EMAIL ADDRESS]`
11+
- Address (optional): `[POSTAL ADDRESS]`
12+
- Date: `[DATE]`
13+
14+
Project:
15+
16+
- `Toolomics`, publicly distributed under the Apache License 2.0
17+
- Maintainer contact for contribution-governance questions: `dr20.spv@listes.cnrs.fr`
18+
19+
By signing this agreement, Contributor confirms that:
20+
21+
1. Contributor has the legal right to submit the contribution.
22+
2. The contribution is an original work of authorship of Contributor, or Contributor otherwise has sufficient rights to submit it.
23+
3. Contributor intentionally submits the contribution for inclusion in `Toolomics` under the Apache License 2.0.
24+
4. Contributor understands that accepted contributions will be publicly distributed under the Apache License 2.0, including its copyright and patent provisions.
25+
5. Contributor is not knowingly submitting material under terms that are incompatible with the Apache License 2.0.
26+
6. Contributor retains ownership of Contributor's copyrights, except for the rights granted through submission under the Apache License 2.0.
27+
7. Nothing in this agreement obligates the project maintainers to accept or use the contribution.
28+
29+
If the contribution is made in the course of employment or under institutional intellectual-property rules, the maintainers may also request `CLA/EMPLOYER_AUTHORIZATION.md`.
30+
31+
Contributor signature:
32+
33+
- Name: `[FULL LEGAL NAME]`
34+
- Signature: `[SIGNATURE]`
35+
- Date: `[DATE]`

‎CONTRIBUTING.md‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,10 @@
1+
# Contributing to Toolomics
2+
3+
Contributor guidance for this repository lives in [`docs/CONTRIBUTING.md`](docs/CONTRIBUTING.md).
4+
5+
Related repository-governance documents:
6+
7+
- [`docs/licensing-notes.md`](docs/licensing-notes.md)
8+
- [`docs/cla-process.md`](docs/cla-process.md)
9+
- [`CLA/INDIVIDUAL_CLA.md`](CLA/INDIVIDUAL_CLA.md)
10+
- [`CLA/EMPLOYER_AUTHORIZATION.md`](CLA/EMPLOYER_AUTHORIZATION.md)

‎LICENSE‎

Lines changed: 201 additions & 0 deletions
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.

‎NOTICE.txt‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
Toolomics
2+
3+
Copyright Centre national de la recherche scientifique (CNRS) and contributors to the Toolomics project.
4+
5+
This product includes software developed for the Toolomics project.
6+
See the LICENSE file for the full Apache License, Version 2.0 text.

‎README.md‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -306,3 +306,7 @@ The deployment script will automatically:
306306
### Learn More
307307

308308
For detailed documentation on `fastmcp`, visit the [fastmcp GitHub repository](https://github.com/jlowin/fastmcp).
309+
310+
## License
311+
312+
Toolomics is distributed under the Apache License 2.0. See [LICENSE](LICENSE), [NOTICE.txt](NOTICE.txt), [`docs/licensing-notes.md`](docs/licensing-notes.md), and [`docs/CONTRIBUTING.md`](docs/CONTRIBUTING.md) for the repository licensing and contribution terms.

‎docs/CONTRIBUTING.md‎

Lines changed: 25 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,25 @@
1+
# Contributing to Toolomics
2+
3+
Thank you for your interest in contributing.
4+
5+
For project setup and deployment details, see `README.md`.
6+
7+
## Licensing and Contributor Agreement
8+
9+
This repository is publicly distributed under the Apache License 2.0.
10+
11+
All non-trivial external contributions require a signed short Individual Contributor Agreement before they can be merged. If a contribution is made in the course of employment or under institutional intellectual-property rules, maintainers may also request the optional Employer / Institutional Authorization.
12+
13+
By submitting a contribution, you confirm that you have the legal right to submit it and that the contribution is intended for inclusion in the Apache License 2.0 codebase.
14+
15+
Accepted contributions are merged into the public Apache License 2.0 repository. The contribution process is intended to confirm submission authority and Apache compatibility; it does not require copyright assignment.
16+
17+
If you are contributing in the course of employment or on behalf of an institution/company, contact `dr20.spv@listes.cnrs.fr` before (or when) opening a pull request.
18+
19+
## CLA Workflow in Pull Requests
20+
21+
- Non-trivial external pull requests require the short Individual Contributor Agreement before merge.
22+
- The optional Employer / Institutional Authorization is requested only when maintainers need confirmation from an employer or institution.
23+
- The CLA Assistant Lite workflow prompts contributors for the individual agreement directly in the PR thread/checks.
24+
- The `CLA Check` status check must pass before merge.
25+
- Contact: `dr20.spv@listes.cnrs.fr`

0 commit comments

Comments
 (0)