Align 1952 with main

.github/workflows/documentation-build.yaml

@@ -14,15 +14,15 @@ jobs:
         - '3.12'
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        pip install -r rtd-requirements.txt
     - name: Build HTML docs with Sphinx
       run: |
         sphinx-build docs/source docs/build/html

.github/workflows/release.yaml

@@ -0,0 +1,60 @@
+---
+# The standard xchem Python package release process.
+# Run on 'Release' and published to PyPI as a 'trusted' publisher.
+#
+# See https://docs.pypi.org/trusted-publishers/creating-a-project-through-oidc/
+# See https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+name: Release
+
+on:
+  release:
+    types:
+    - published
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v6
+      with:
+        persist-credentials: false
+    - name: Inject slug/short variables
+      uses: rlespinasse/github-slug-action@v5
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.x'
+    - name: Install build package
+      run: |
+        pip install --upgrade pip
+        pip install uv --user
+    - name: Build
+      run: |
+        uv version $GITHUB_REF_SLUG
+        uv build
+    - name: Store the distribution
+      uses: actions/upload-artifact@v5
+      with:
+        name: python-package-distribution
+        path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/xchem-fragalysis
+    permissions:
+      id-token: write
+    steps:
+    - name: Download distribution
+      uses: actions/download-artifact@v6
+      with:
+        name: python-package-distribution
+        path: dist/
+    - name: Publish
+      uses: pypa/gh-action-pypi-publish@release/v1

.readthedocs.yaml

@@ -24,4 +24,4 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
   install:
-   - requirements: requirements.txt
+  - requirements: requirements.txt

README.md

@@ -1,6 +1,9 @@
 # Fragalysis
 
-![documentation build](https://github.com/xchem/fragalysis/workflows/documentation%20build/badge.svg)
+![PyPI - Version](https://img.shields.io/pypi/v/xchem-fragalysis)
+
+![documentation build](https://github.com/xchem/fragalysis/actions/workflows/documentation-build.yaml/badge.svg)
+![release](https://github.com/xchem/fragalysis/actions/workflows/release.yaml/badge.svg)
 
 ![RTD latest build](https://readthedocs.org/projects/fragalysis/badge/?version=latest&style=plastic)
 
@@ -13,7 +16,7 @@ as a 'base' for all documentation relating to the application.
 >   This replaces the original fragalysis repository, which was responsible for the
     RDKit-based Python tools for analysis of protein-ligand interactions.
     The original repository has been renamed and can now be found in the
-    [fragalysis-package] repository.
+    [fragutils] repository.
 
 The repository is compatible with ReadTheDocs and you can find the latest documentation
 (built from the most recent changes on this repository's `main` branch) on [ReadTheDocs] at
@@ -22,16 +25,42 @@ https://fragalysis.readthedocs.io/en/latest/.
 Stable documentation (built from the most recent tag in this repository) can be found at
 https://fragalysis.readthedocs.io/en/stable/.
 
+## XChem repositories
+A significant amount of our work resides in public GitHub repositories in the
+`XChem` organisation. A growing list of all the repositories that represent
+our work can be found in the **Related repositories** section below. We also rely on a
+number of _external_ repositories (those not managed by us directly). Importantly,
+when we find that the material in such a repository becomes crucial to our work we
+**SHOULD** consider *fork* it to `XChem`. Forking allows us to: -
+
+- Preserve content
+- Adopt our own development processes, which include: -
+  - A consistent release mechanism
+  - Consistent package naming (PyPI packages all begin `xchem-` for example)
+  - Use of linting, formatting, and test tools that we like
+- Improve stability (we like working with static *tagged* references)
+
+In `xchem` we tend to follow a trunk-based development strategy that we explain in
+our [trunk-based-development] repository. It's provides us with a centrally-defined
+set of policies with accompanying documentation on its [wiki] - a place
+where we provide guidance, some advanced topics, and development inspiration.
+
+**Working on codes that's not in XChem?**
+
+If you are using code that we don't own (manage) we **MUST** consider forking the
+repository into `XChem`, applying our development process, tagging it when important
+changes are available, and asking others to switch to using our repository and the
+packages it produces.
+
 ## Local development
 To compile the documentation, which is based on [Sphinx],
 start with a Python environment (ideally Python 3.12, as that's the version used by
 ReadTheDocs and the GitHub CI workflow) and install the dependencies: -
 
-    python -m venv venv
-    source venv/bin/activate
-    pip install --upgrade pip
-
-    pip install -r requirements.txt
+    pip install uv
+    uv venv
+    source .venv/bin/activate
+    pip install -r rtd-requirements.txt
 
 Then, to build the HTML documentation, run the following command: -
 
@@ -44,9 +73,11 @@ The Fragalysis Stack you find running in Kubernetes relies on a number of relate
 (and diverse) repositories. We've tried to capture references to all of them
 below, in no particular order: -
 
-**xchem respositories**
+**xchem repositories**
 
-[fragalysis-package] : Logic that allows connection to the neo4j graph
+[trunk-based-development] : A repository for development guidance
+
+[fragutils] : Logic that allows connection to the neo4j graph
 
 [fragalysis-backend] : Django/REST Framework application
 
@@ -57,7 +88,10 @@ to create the container image
 
 [fragalysis-api] : Command-line API utilities
 
+[fragalysis-database] : A reference PostgreSQL database image (with extras)
+
 [fragalysis-keycloak] : A specialised build of keycloak to provide a custom login theme
+deprecated
 
 [fragalysis-ispyb-target-access-authenticator] : Code for the container image that acts
 as an interface to ISPyB, yielding Target Access Strings based on username
@@ -136,11 +170,14 @@ typically kubernetes or slurm: -
 [fragalysis-ispyb-target-access-authenticator]: https://github.com/xchem/fragalysis-ispyb-target-access-authenticator
 [fragalysis-rdkit-cartridge-pgvector-debian]: https://github.com/xchem/fragalysis-rdkit-cartridge-pgvector-debian
 [fragalysis-api]: https://github.com/xchem/fragalysis-api
+[fragalysis-database]: https://github.com/xchem/fragalysis-database
 [fragalysis-backend]: https://github.com/xchem/fragalysis-backend
 [fragalysis-frontend]: https://github.com/xchem/fragalysis-frontend
 [fragalysis-keycloak]: https://github.com/xchem/fragalysis-keycloak
-[fragalysis-package]: https://github.com/xchem/fragalysis-package
+[fragutils]: https://github.com/xchem/fragutils
 [fragalysis-stack]: https://github.com/xchem/fragalysis-stack
 [readthedocs]: https://app.readthedocs.org/dashboard/
 [sphinx]: https://www.sphinx-doc.org/en/master
+[trunk-based-development]: https://github.com/xchem/trunk-based-development
 [xchem-align]: https://github.com/xchem/xchem-align
+[wiki]: https://github.com/xchem/trunk-based-development/wiki

docs/source/changelog.md

@@ -12,9 +12,40 @@
 ![GitHub last commit](https://img.shields.io/github/last-commit/xchem/fragalysis-frontend?style=for-the-badge&label=last%20f%2Fe%20update)
 
 
-
 ## Release Notes
 
+- [2026.02.1](https://github.com/xchem/fragalysis-stack/releases/tag/2026.02.1)
+  * 1997 [Results (former scores) invisible after unification](https://github.com/m2ms/fragalysis-frontend/issues/1997)
+  * 1998 [Change version mismatch message (XCAv3)](https://github.com/m2ms/fragalysis-frontend/issues/1998)
+  * 2003 [Incorrectly assigned shortcodes](https://github.com/m2ms/fragalysis-frontend/issues/2003)
+  * 2028 [Target loader no main_observation error](https://github.com/m2ms/fragalysis-frontend/issues/2028)
+- [2026.01.1](https://github.com/xchem/fragalysis-stack/releases/tag/2026.01.1)
+  * 1908 [Mpro download fails with 403](https://github.com/m2ms/fragalysis-frontend/issues/1908)
+  * 1922 [Major backend dependency upgrade](https://github.com/m2ms/fragalysis-frontend/issues/1922)
+  * 1932 [More options to download endpoint (e.g. sqlite files)](https://github.com/m2ms/fragalysis-frontend/issues/1932)
+  * 1934 [Squonk file transfer fails if no proteins supplied](https://github.com/m2ms/fragalysis-frontend/issues/1934)
+  * 1935 [Incorrect ligand file path handling in target loader](https://github.com/m2ms/fragalysis-frontend/issues/1935)
+  * 1936 [Missing snapshot thumbnails](https://github.com/m2ms/fragalysis-frontend/issues/1936)
+  * 1938 [Assay data upload bug](https://github.com/m2ms/fragalysis-frontend/issues/1938)
+  * 1939 [Fix __str__ method AttributeError](https://github.com/m2ms/fragalysis-frontend/issues/1939)
+  * 1944 [Changes to plot_data endpoint](https://github.com/m2ms/fragalysis-frontend/issues/1944)
+  * 1955 [Target loader support for v3 XCA data format](https://github.com/m2ms/fragalysis-frontend/issues/1955)
+  * 1966 [Path file restoration for v2 data (post-v3 migration)](https://github.com/m2ms/fragalysis-frontend/issues/1966)
+  * 1981 [Investigate OSV scanner during build](https://github.com/m2ms/fragalysis-frontend/issues/1981)
+  * 1991 [Remove Sentry error transmission?](https://github.com/m2ms/fragalysis-frontend/issues/1991)
+  * 1992 [Fix v3 data loading](https://github.com/m2ms/fragalysis-frontend/issues/1992)
+  * 2002 [Make cset upload ignore superseded observations](https://github.com/m2ms/fragalysis-frontend/issues/2002)
+  * 1598 https://github.com/m2ms/fragalysis-frontend/issues/1598
+  * 1819 https://github.com/m2ms/fragalysis-frontend/issues/1819
+  * 1889 [Expand observation column on first target load](https://github.com/m2ms/fragalysis-frontend/issues/1989)
+  * 1912 https://github.com/m2ms/fragalysis-frontend/issues/1912
+  * 1936 https://github.com/m2ms/fragalysis-frontend/issues/1936
+  * 1945 https://github.com/m2ms/fragalysis-frontend/issues/1945
+  * 1960 https://github.com/m2ms/fragalysis-frontend/issues/1960
+  * 1965 https://github.com/m2ms/fragalysis-frontend/issues/1965
+  * 1967 https://github.com/m2ms/fragalysis-frontend/issues/1967
+  * 1969 https://github.com/m2ms/fragalysis-frontend/issues/1969
+  * 1974 https://github.com/m2ms/fragalysis-frontend/issues/1974
 - [2025.11.1](https://github.com/xchem/fragalysis-stack/releases/tag/2025.10.3)
 	* _FEATURE_ [Filtering by geometric coordinates](https://github.com/m2ms/fragalysis-frontend/issues/1821)
 	* _IMPROVEMENT_ [More options to download endpoint (e.g. sqlite files)](https://github.com/m2ms/fragalysis-frontend/issues/1932)

docs/source/py_api.md

@@ -20,7 +20,7 @@ pip install --user -e .
 To get a list of target dictionaries accessible with an optional authentication token:
 
 ```
-from fragalysis.requests.download import target_list
+from fragalysis.requests import target_list
 targets = target_list(stack="production", token=token)
 ```
 
@@ -31,7 +31,7 @@ The `token` keyword can be ommitted if only accessing public targets, and `stack
 To get a list of target dictionaries accessible with an optional authentication token:
 
 ```
-from fragalysis.requests.download import download_target
+from fragalysis.requests import download_target
 download_target(name=target_name, tas=target_access_string, token=token, stack="production", destination=".")
 ```
 
@@ -47,6 +47,34 @@ The available POST request parameters to `/api/download_structures` can be seen
 Relevant developer contacts on github are @mwinokan, @kaliif, and @boriskovar-m2ms.
 ```
 
+## Tracking experiment uploads
+
+For the purpose of automated scraping you can use the `target_uploads` function to see if there have been any recent uploads:
+
+```
+uploads = target_uploads(statistics_only=True)
+```
+
+This returns a dictionary keyed by (target_name, target_access_string):
+
+```
+{
+    ('A71EV2A', 'lb32627-66'): {
+        'target_id': 31,
+        'target_name': 'A71EV2A',
+        'target_access_string': 'lb32627-66',
+        'project_id': 1,
+        'last_upload_index': 8,
+        'last_upload_timestamp': datetime.datetime(2025, 10, 8, 12, 34, 0, 693173, tzinfo=datetime.timezone.utc)
+    },
+    ...
+}
+```
+
+You can then check `last_upload_index` against your most recent download, or use `last_upload_timestamp` to determine if a fresh download is needed.
+
+Then use the `download_target` function as described above.
+
 ## API reference
 
 ```{autodoc2-summary}

fragalysis/requests/__init__.py

@@ -1,4 +1,4 @@
-from .download import target_list, download_target
+from .download import target_list, download_target, target_uploads
 from .csets import upload_sdf
 from .plotly import upload_graph
 from .fragmenstein import fragmenstein_place, fragmenstein_combine

fragalysis/requests/download.py

@@ -7,7 +7,7 @@
 from urllib.parse import urljoin
 
 from .session import _session
-from .urls import PROJECTS_URL, TARGETS_URL, DOWNLOAD_URL
+from .urls import PROJECTS_URL, TARGETS_URL, DOWNLOAD_URL, TARGET_EXPERIMENT_UPLOADS_URL
 
 
 def target_list(
@@ -239,3 +239,85 @@ def download_target(
             return None
 
     return target_dir
+
+
+def target_uploads(
+    stack: str = "production",
+    token: str | None = None,
+    statistics_only: bool = False,
+) -> dict[(str,str), list]:
+    """Request a dictionary of uploads keyed by target name and target_access_strings from a Fragalysis deployment
+
+    :param stack: shorthand or URL of Fragalysis deployment, defaults to "production"
+    :param token: optional authentication token
+    :param statistics_only: don't list individual uploads
+    :returns: list of target upload dictionaries with "id", "title", and "project" keys
+    """
+
+    from datetime import datetime
+
+    with _session(stack, token) as session:
+
+        # get the API response
+
+        url = urljoin(session.root, TARGET_EXPERIMENT_UPLOADS_URL)
+
+        response = session.get(url)
+
+        if not response.ok:
+            mrich.error("Request failed", url, response.status_code)
+            return None
+
+        data = response.json()
+
+        # group the data by (target_name, proposal_number)
+
+        formatted = {}
+        for d in data["results"]:
+
+            key = (d["target_name"], d["proposal_number"])
+
+            formatted.setdefault(key, {})
+            formatted[key].setdefault("uploads", [])
+
+            formatted[key]["target_id"]=d["target"]
+            formatted[key]["target_name"]=d["target_name"]
+            formatted[key]["target_access_string"]=d["proposal_number"]
+            formatted[key]["project_id"]=d["project"]
+
+            # reformat the serialised data
+
+            formatted[key]["uploads"].append(dict(
+                xca_tarball_url=d["tarball"],
+                committer_id=d["committer"],
+                committer_name=d["committer_name"],
+                upload_index=d["upload_version"],
+                data_format=f"{d['data_version_major']}.{d['data_version_minor']}",
+                timestamp=datetime.fromisoformat(d["commit_datetime"].replace("Z", "+00:00")),
+            ))
+
+    # sort and format the data
+
+    for key, d in formatted.items():
+
+        new_d = {}
+
+        # general information
+        new_d["target_id"]=d["target_id"]
+        new_d["target_name"]=d["target_name"]
+        new_d["target_access_string"]=d["target_access_string"]
+        new_d["project_id"]=d["project_id"]
+
+        # sort uploads
+        sorted_uploads = sorted(d["uploads"], key=lambda d: d["upload_index"])
+
+        # latest statistics
+        new_d["last_upload_index"]=sorted_uploads[-1]["upload_index"]
+        new_d["last_upload_timestamp"]=sorted_uploads[-1]["timestamp"]
+
+        if not statistics_only:
+            new_d["uploads"] = sorted_uploads
+
+        formatted[key] = new_d
+
+    return formatted

fragalysis/requests/urls.py

@@ -20,3 +20,4 @@
 TASK_STATUS_URL = "/viewer/task_status/"
 USER_URL = "/api/user"
 PLOT_DATA_URL = "/api/plot_data/"
+TARGET_EXPERIMENT_UPLOADS_URL = "/api/target_experiment_uploads/"