diff --git a/.github/workflows/documentation-build.yaml b/.github/workflows/documentation-build.yaml index fe70535..5457a97 100644 --- a/.github/workflows/documentation-build.yaml +++ b/.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 diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml new file mode 100644 index 0000000..45ab575 --- /dev/null +++ b/.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 diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 9ca9147..def6f02 100644 --- a/.readthedocs.yaml +++ b/.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 diff --git a/README.md b/README.md index c98330a..d0739ef 100644 --- a/README.md +++ b/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 diff --git a/docs/source/changelog.md b/docs/source/changelog.md index 5bd86c2..a06c051 100644 --- a/docs/source/changelog.md +++ b/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) diff --git a/docs/source/py_api.md b/docs/source/py_api.md index 2b5ab61..fadbb09 100644 --- a/docs/source/py_api.md +++ b/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} diff --git a/fragalysis/requests/__init__.py b/fragalysis/requests/__init__.py index 7c0d3c4..58f981c 100644 --- a/fragalysis/requests/__init__.py +++ b/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 diff --git a/fragalysis/requests/download.py b/fragalysis/requests/download.py index b7bfea8..74c676a 100644 --- a/fragalysis/requests/download.py +++ b/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 diff --git a/fragalysis/requests/urls.py b/fragalysis/requests/urls.py index 1cdc3d8..6597b69 100644 --- a/fragalysis/requests/urls.py +++ b/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/" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..af09667 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,42 @@ +[build-system] +requires = ["setuptools>=82.0.0"] +build-backend = "setuptools.build_meta" + +[project] +name = "xchem-fragalysis" +version = "0.0.0" +description = "Python module to interact with Fragalysis" +readme = "README.md" +keywords = ["api"] +license = "MIT" +license-files = ["LICENSE"] +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Environment :: Console", + "Intended Audience :: Developers", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", + "Topic :: System :: Installation/Setup", + "Operating System :: POSIX :: Linux", +] +authors = [ + {name = "Alan Christie", email = "achristie@informaticsmatters.com"}, +] +maintainers = [ + {name = "Alan Christie", email = "achristie@informaticsmatters.com"}, +] +requires-python = ">=3.11" +dependencies = [ + "gemmi>=0.7.5", + "im-squonk2-client>=6.1.0,<7", + "ipywidgets>=8.1.8,<9", + "mypytools>=0.1.15", + "pandas>=3.0.1,<4", + "rdkit==2025.9.6", + "xchem-molparse>=1.0.0,<2", +] + +[project.urls] +Repository = "https://github.com/xchem/fragalysis.git" diff --git a/requirements.txt b/rtd-requirements.txt similarity index 100% rename from requirements.txt rename to rtd-requirements.txt diff --git a/setup.py b/setup.py deleted file mode 100644 index 2c15f66..0000000 --- a/setup.py +++ /dev/null @@ -1,11 +0,0 @@ -from setuptools import setup - -setup( - name='fragalysis', - version='1.0', - 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