bastonero · vdemestral · Jan 17, 2025 · Jan 17, 2025
diff --git a/.cla/version1/CLA.md b/.cla/version1/CLA.md
@@ -0,0 +1,102 @@
+# Contributor License Agreement
+
+> Adapted from the [Apache Software Foundation Individual Contributor License Agreement (ICLA)](https://www.apache.org/licenses/contributor-agreements.html) [version 2.2](https://www.apache.org/licenses/icla.pdf)
+
+You accept and agree to the following terms and conditions for Your
+Contributions (present and future) that you submit to the copyright
+holders (hereafter "HOLDERS", see the [`LICENSE.txt`](../../LICENSE.txt)
+bundled with this software). In return, the HOLDERS shall not use
+Your Contributions in a way that is contrary to the public benefit or
+inconsistent with its nonprofit status and bylaws in effect at the
+time of the Contribution. Except for the license granted herein to
+the HOLDERS and recipients of software distributed by the HOLDERS,
+You reserve all right, title, and interest in and to Your Contributions.
+
+1. Definitions.
+
+    "You" (or "Your") shall mean the copyright owner or legal entity
+    authorized by the copyright owner that is making this Agreement
+    with the HOLDERS. For legal entities, the entity making a
+    Contribution and all other entities that control, are controlled
+    by, or are under common control with that entity are considered to
+    be a single Contributor. For the purposes of this definition,
+    "control" means (i) the power, direct or indirect, to cause the
+    direction or management of such entity, whether by contract or
+    otherwise, or (ii) ownership of fifty percent (50%) or more of the
+    outstanding shares, or (iii) beneficial ownership of such entity.
+    "Contribution" shall mean any original work of authorship,
+    including any modifications or additions to an existing work, that
+    is intentionally submitted by You to the HOLDERS for inclusion
+    in, or documentation of, any of the products owned or managed by
+    the HOLDERS (the "Work"). For the purposes of this definition,
+    "submitted" means any form of electronic, verbal, or written
+    communication sent to the HOLDERS or its representatives,
+    including but not limited to communication on electronic mailing
+    lists, source code control systems, and issue tracking systems that
+    are managed by, or on behalf of, the HOLDERS for the purpose of
+    discussing and improving the Work, but excluding communication that
+    is conspicuously marked or otherwise designated in writing by You
+    as "Not a Contribution."
+
+2. Grant of Copyright License. Subject to the terms and conditions of
+    this Agreement, You hereby grant to the HOLDERS and to
+    recipients of software distributed by the HOLDERS a perpetual,
+    worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+    copyright license to reproduce, prepare derivative works of,
+    publicly display, publicly perform, sublicense, and distribute Your
+    Contributions and such derivative works.
+
+3. Grant of Patent License. Subject to the terms and conditions of
+    this Agreement, You hereby grant to the HOLDERS and to
+    recipients of software distributed by the HOLDERS a perpetual,
+    worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+    (except as stated in this section) patent license to make, have
+    made, use, offer to sell, sell, import, and otherwise transfer the
+    Work, where such license applies only to those patent claims
+    licensable by You that are necessarily infringed by Your
+    Contribution(s) alone or by combination of Your Contribution(s)
+    with the Work to which such Contribution(s) was submitted. If any
+    entity institutes patent litigation against You or any other entity
+    (including a cross-claim or counterclaim in a lawsuit) alleging
+    that your Contribution, or the Work to which you have contributed,
+    constitutes direct or contributory patent infringement, then any
+    patent licenses granted to that entity under this Agreement for
+    that Contribution or Work shall terminate as of the date such
+    litigation is filed.
+
+4. You represent that you are legally entitled to grant the above
+    license. If your employer(s) has rights to intellectual property
+    that you create that includes your Contributions, you represent
+    that you have received permission to make Contributions on behalf
+    of that employer, that your employer has waived such rights for
+    your Contributions to the HOLDERS, or that your employer has
+    executed a separate Corporate CLA with the HOLDERS.
+
+5. You represent that each of Your Contributions is Your original
+    creation (see section 7 for submissions on behalf of others). You
+    represent that Your Contribution submissions include complete
+    details of any third-party license or other restriction (including,
+    but not limited to, related patents and trademarks) of which you
+    are personally aware and which are associated with any part of Your
+    Contributions.
+
+6. You are not expected to provide support for Your Contributions,
+    except to the extent You desire to provide support. You may provide
+    support for free, for a fee, or not at all. Unless required by
+    applicable law or agreed to in writing, You provide Your
+    Contributions on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS
+    OF ANY KIND, either express or implied, including, without
+    limitation, any warranties or conditions of TITLE, NON-
+    INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE.
+
+7. Should You wish to submit work that is not Your original creation,
+    You may submit it to the HOLDERS separately from any
+    Contribution, identifying the complete details of its source and of
+    any license or other restriction (including, but not limited to,
+    related patents, trademarks, and license agreements) of which you
+    are personally aware, and conspicuously marking the work as
+    "Submitted on behalf of a third-party: [named here]".
+
+8. You agree to notify the HOLDERS of any facts or circumstances of
+    which you become aware that would make these representations
+    inaccurate in any respect.
diff --git a/.cla/version1/signatures.json b/.cla/version1/signatures.json
@@ -0,0 +1,20 @@
+{
+  "signedContributors": [
+    {
+      "name": "bastonero",
+      "id": 79980269,
+      "comment_id": 2343829130,
+      "created_at": "2024-09-11T14:22:56Z",
+      "repoId": 390674389,
+      "pullRequestNo": 78
+    },
+    {
+      "name": "vdemestral",
+      "id": 114935148,
+      "comment_id": 2580462168,
+      "created_at": "2025-01-09T14:49:31Z",
+      "repoId": 390674389,
+      "pullRequestNo": 67
+    }
+  ]
+}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -37,7 +37,7 @@ jobs:
 
         strategy:
             matrix:
-                python-version: ['3.10']
+                python-version: ['3.10','3.12']
 
         services:
             rabbitmq:
@@ -68,4 +68,13 @@ jobs:
         -   name: Run pytest
             env:
                 AIIDA_WARN_v3: 1
-            run: pytest -sv tests
+            run: pytest -sv --cov aiida_vibroscopy tests
+
+        -   name: Upload to Codecov
+            if: matrix.python-version == 3.10
+            uses: codecov/codecov-action@v3
+            with:
+                token: ${{ secrets.CODECOV_TOKEN }}
+                name: pytests-vibroscopy3.10
+                flags: pytests
+                fail_ci_if_error: true
diff --git a/.github/workflows/cla.yml b/.github/workflows/cla.yml
@@ -0,0 +1,55 @@
+name: "CLA Assistant"
+on:
+  issue_comment:
+    types: [created]
+  pull_request_target:
+    types: [opened, closed, synchronize]
+
+# explicitly configure permissions, in case your GITHUB_TOKEN workflow permissions are set to read-only in repository settings
+permissions:
+  actions: write
+  contents: write
+  pull-requests: write
+  statuses: write
+
+jobs:
+  CLAAssistant:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.APP_ID }}
+          private-key: ${{ secrets.PRIVATE_KEY }}
+
+      - uses: contributor-assistant/github-action@v2.4.0
+        if: (github.event.comment.body == 'recheck' || github.event.comment.body == 'I have read the CLA Document and I hereby accept the CLA') || github.event_name == 'pull_request_target'
+        env:
+          # the default github token does not allow github action to create & push commit,
+          # instead, we need to use a github app to generate a token
+          # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ steps.app-token.outputs.token }}
+          # the below token should have repo scope and must be manually added by you in the repository's secret
+          # This token is required only if you have configured to store the signatures in a remote repository/organization
+          # PERSONAL_ACCESS_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
+        with:
+          path-to-signatures: ".cla/version1/signatures.json"
+          path-to-document: "https://github.com/bastonero/aiida-vibroscopy/blob/main/.cla/version1/CLA.md"
+          # branch should not be protected
+          branch: "main"
+          allowlist: bot*
+
+          # the followings are the optional inputs - If the optional inputs are not given, then default values will be taken
+          #remote-organization-name: enter the remote organization name where the signatures should be stored (Default is storing the signatures in the same repository)
+          #remote-repository-name: enter the  remote repository name where the signatures should be stored (Default is storing the signatures in the same repository)
+          #create-file-commit-message: 'For example: Creating file for storing CLA Signatures'
+          #signed-commit-message: 'For example: $contributorName has signed the CLA in $owner/$repo#$pullRequestNo'
+          custom-notsigned-prcomment: 'Thank you for your submission, we really appreciate it. Like many open-source projects, we ask that you accept our [Contributor License Agreement](https://github.com/bastonero/aiida-vibroscopy/blob/main/.cla/version1/CLA.md) before we can merge your contribution. You can accept the CLA by just copying the sentence below and posting it as a Pull Request Comment.'
+          custom-pr-sign-comment: 'I have read the CLA Document and I hereby accept the CLA'
+          custom-allsigned-prcomment: |
+            All contributors have accepted the CLA ✅
+
+            ---
+            <sub>You might need to click the "Update/Rebase branch" button to update the pull request and rerun the GitHub actions to pass the CLA check.</sub>
+          #lock-pullrequest-aftermerge: false - if you don't want this bot to automatically lock the pull request after merging (default - true)
+          #use-dco-flag: true - If you are using DCO instead of CLA
diff --git a/.github/workflows/update_changelog.py b/.github/workflows/update_changelog.py
@@ -0,0 +1,85 @@
+#!/bin/bash
+# -*- coding: utf-8 -*-
+"""Script for automatically updating the `CHANGELOG.md` based on the commits since the latest release tag."""
+from pathlib import Path
+import re
+import subprocess
+
+DEFAULT_CHANGELOG_SECTIONS = """
+### ‼️ Breaking changes
+
+
+### ✨ New features
+
+
+### 🗑️ Deprecations
+
+
+### 👌 Improvements
+
+
+### 🐛 Bug fixes
+
+
+### 📚 Documentation
+
+
+### 🔧 Maintenance
+
+
+### ⬆️ Update dependencies
+
+
+### ♻️ Refactor
+
+"""
+
+
+def update_changelog():
+    """Update the `CHANGELOG.md` for a first draft of the release."""
+    print('🔍 Checking the current version number')
+    current_changelog = Path('CHANGELOG.md').read_text(encoding='utf-8')
+
+    from aiida_vibroscopy import __version__
+
+    if str(__version__) in current_changelog:
+        print('🛑 Current version already in `CHANGELOG.md`. Skipping...')
+        return
+
+    print('⬆️ Found updated version number, adapting `CHANGELOG.md`.')
+    tags = subprocess.run(['git', 'tag', '--sort=v:refname'], capture_output=True, check=True, encoding='utf-8').stdout
+    latest_tag = re.findall(r'(v\d\.\d\.\d)\n', tags)[-1]
+
+    print(f'🔄 Comparing with latest tag `{latest_tag}`.')
+    commits = subprocess.run(['git', 'log', "--pretty=format:'%h|%H|%s'", f'{latest_tag}..origin/main'],
+                             capture_output=True,
+                             check=True,
+                             encoding='utf-8').stdout
+
+    pr_pattern = re.compile(r'\(\S(?P<pr_number>\d+)\)')
+
+    changelog_message = f'## v{__version__}\n' + DEFAULT_CHANGELOG_SECTIONS
+
+    for commit in commits.splitlines():
+
+        # Remove the PR number from the commit message
+        pr_match = pr_pattern.search(commit)
+
+        if pr_match is not None:
+            pr_number = pr_match.groupdict()['pr_number']
+            commit = commit.replace(fr'(#{pr_number})', '')
+
+        # Add the commit hash (short) to link to the changelog
+        commit = commit.strip("'")
+        hash_short, hash_long, message = commit.split('|', maxsplit=2)
+        message += f'[[{hash_short}](https://github.com/aiidateam/aiida-quantumespresso/commit/{hash_long})]'
+        changelog_message += f'\n* {message}'
+
+    with Path('CHANGELOG.md').open('w', encoding='utf8') as handle:
+        handle.write(changelog_message + '\n\n' + current_changelog)
+
+    print("🚀 Success! Finalise the `CHANGELOG.md` and let's get this baby released.")
+
+
+if __name__ == '__main__':
+    update_changelog()
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,85 @@
+## v1.1.1
+
+This minor release adds the new AiiDA contributor license agreement (CLA), and its GitHub bot,
+along with some dependency contraints for phonopy. The latest versions of phonopy (>v2.26)
+break the tests. While figuring out why, we patch this until a solution is found.
+
+### 🐛 Bug fixes
+
+* Deps: constrain phonopy and spglib versions [[3a3e3d1](https://github.com/aiidateam/aiida-quantumespresso/commit/3a3e3d117e34c6a66fcdc74e1e21c6263c203565)]
+
+### 📚 Documentation
+
+* Fix some docstrings and reports [[3ee9e7c](https://github.com/aiidateam/aiida-quantumespresso/commit/3ee9e7cbd2f5e6b8f15229dafbed58ae7ef4fa0d)]
+* Update main paper reference[[504c1b7](https://github.com/aiidateam/aiida-quantumespresso/commit/504c1b7b65a8852395d0ff3ec7271cb8c05c6931)]
+
+### 🔧 Maintenance
+
+* CLA: update and remove old cla-bot [[32bd829](https://github.com/aiidateam/aiida-quantumespresso/commit/32bd829987751deba056b7bfa739f6c82cf89d3e)]
+* @bastonero has signed the CLA in bastonero/aiida-vibroscopy#78[[e83739f](https://github.com/aiidateam/aiida-quantumespresso/commit/e83739f6aaecfcb304f8cac3da6d54b93f0fafb7)]
+* Add the AiiDA CLA [[df2cade](https://github.com/aiidateam/aiida-quantumespresso/commit/df2cade1bf200b8a2dd7004a48e40b118257f134)]
+* Add CLA bot [[3ba3e9e](https://github.com/aiidateam/aiida-quantumespresso/commit/3ba3e9e9f094106254b1a8ee4c97b85e66b41f85)]
+
+### ⬆️ Update dependencies
+
+* Deps: constrain phonopy and spglib versions [[3a3e3d1](https://github.com/aiidateam/aiida-quantumespresso/commit/3a3e3d117e34c6a66fcdc74e1e21c6263c203565)]
+
+
+
+
+## v1.1.0
+
+This minor release includes new post-processing utilities, a small breaking change in [[42503f3]](https://github.com/bastonero/aiida-vibroscopy/commit/42503f312d9a812cfc46d4c4a03a78641201e1d3) with regards to reference system for non-analytical and polarization directions. Some examples providing
+a unique python script to run the `IRamanSpectraWorkChain` are also added to help new users to get started. The license terms are also updated.
+A CHANEGELOG file is finally added to keep track in a pretty format of the changes among releases of the code.
+
+The new post-processing utilities can be used directly through a `VibrationalData` node, in a similar fashion to the other methods.
+For instance, to compute the complex dielectric matrix and the normal reflectivity in the infrared regime:
+
+```python
+node = load_node(PK) # PK to a VibrationalData node
+
+complex_dielectric = node.run_complex_dielectric_function() # (3,3,num_steps) shape complex array; num_steps are the number of frequency points where the function is evaluated
+reflectivity = node.run_normal_reflectivity_spectrum([0,0,1]) # (frequency points, reflectance value), [0,0,1] is the orthogonal direction index probed via q.eps.q
+```
+
+Now, the polarization and non-analytical directions in _all_ methods in aiida-vibroscopy should be given in Cartesian coordinates:
+
+```python
+node = load_node(PK) # PK to a VibrationalData node
+
+scattering_geometry = dict(pol_incoming=[1,0,0], pol_outgoing=[1,0,0], nac_direction=[0,0,1]) # corresponding to ZXXZ scattering setup
+intensities, frequencies, mode_symmetry_labels = node.run_single_crystal_raman_intensities(**scattering_geometry)
+```
+
+### ‼️ Breaking changes
+
+* Post-processing: polarization and nac directions in Cartesian coordinates [[42503f3]](https://github.com/bastonero/aiida-vibroscopy/commit/42503f312d9a812cfc46d4c4a03a78641201e1d3)
+
+### 👌 Improvements
+
+* Post-processing: computation of complex dielectric function and normal reflectivity in the infrared [[42503f3]](https://github.com/bastonero/aiida-vibroscopy/commit/42503f312d9a812cfc46d4c4a03a78641201e1d3)
+* `Examples`: new folder with working examples for different use cases to get new users started [[7deb31b]](https://github.com/bastonero/aiida-vibroscopy/commit/7deb31b5f547ca16e4522be960b4aa5bbe13fccf)
+* CI: add codecov step [[f36e8a1]](https://github.com/bastonero/aiida-vibroscopy/commit/f36e8a10566af68843546bae428560dff393aaf1)
+
+### 🐛 Bug Fixes
+
+* `Docs`: fix typos [[85b1830]](https://github.com/bastonero/aiida-vibroscopy/commit/85b18305be6e7e76efce35d9e4ae4c5a3547f9bc), [[e924b3d]](https://github.com/bastonero/aiida-vibroscopy/commit/e924b3dd436a67192f6c0780ff3a318581ab1fc5)
+* Post-processing: fix coordinates and units [[42503f3]](https://github.com/bastonero/aiida-vibroscopy/commit/42503f312d9a812cfc46d4c4a03a78641201e1d3)
+
+### 📚 Documentation
+
+* Set correct hyperlink for AiiDA paper [[c92994d]](https://github.com/bastonero/aiida-vibroscopy/commit/c92994de36c336a265ac262eea2dc8d77fb11f08)
+
+### 🔧 Maintenance
+
+* Adapt tests also for other changes [[be3a6b7]](https://github.com/bastonero/aiida-vibroscopy/commit/be3a6b7d67926816957634fd7b520cd021532f0f)
+* Add loads of tests [[42503f3]](https://github.com/bastonero/aiida-vibroscopy/commit/42503f312d9a812cfc46d4c4a03a78641201e1d3)
+* `README`: add more information and badges [[c92994d]](https://github.com/bastonero/aiida-vibroscopy/commit/c92994de36c336a265ac262eea2dc8d77fb11f08)
+* Docs: Remove aiida.manage.configuration.load_documentation_profile [[f914cbb]](https://github.com/bastonero/aiida-vibroscopy/commit/f914cbb5460d4f988dd117628890a8f53f1c976a)
+* DevOps: update docs dependencies [[a0d124e]](https://github.com/bastonero/aiida-vibroscopy/commit/a0d124ee24cb287f9d90583b389f38d6b6265b9e)
+* Bump SSSP version to 1.3 in tests [[94c72e5]](https://github.com/bastonero/aiida-vibroscopy/commit/94c72e5183584af08d9874fe2b6fc2ad41fce1b5)
+
+### ⬆️ Update dependencies
+
+* DevOps: update docs dependencies [[a0d124e]](https://github.com/bastonero/aiida-vibroscopy/commit/a0d124ee24cb287f9d90583b389f38d6b6265b9e)