Merge pull request #301 from MannLabs/improve_readme

Improve readme and re-add Docker

Author: mschwoer

.github/workflows/publish_docker_image.yml

@@ -0,0 +1,20 @@
+# Build and publish Docker image
+name: Publish Docker image
+
+on:
+  workflow_dispatch:
+    inputs:
+      tag_to_release:
+        description: 'Enter tag to release (example: v1.5.5). A tag with this name must exist in the repository.'
+        type: string
+        required: true
+
+jobs:
+  publish_on_pypi:
+    uses: MannLabs/alphashared/.github/workflows/publish_docker.yml@v1
+    secrets:
+      docker_access_token: ${{ secrets.DOCKER_ACCESS_TOKEN }}
+      docker_username: ${{ secrets.DOCKER_USERNAME }}
+    with:
+      package_name: alphatims
+      tag_to_release: ${{ inputs.tag_to_release }}

CHANGELOG.md

@@ -0,0 +1,59 @@
+## Release History
+
+For later release, see https://github.com/MannLabs/alphatims/releases
+
+## 1.0.0
+
+  * FEAT: tempmmap for large arrays by default.
+
+## 0.3.2
+
+  * FEAT: cli/gui allow bruker data as argument.
+  * FEAT/FIX: Polarity included in frame table.
+  * FIX: utils cleanup.
+  * FIX: utils issues.
+  * FEAT: by default use -1 threads in utils.
+  * FIX: disable cla check.
+
+## 0.3.1
+
+  * FIX/FEAT: Intensity correction when ICC is used. Note that this is only for exported data, not for visualized data.
+  * FEAT: By default, hdf files are now mmapped, making them much faster to initially load and use virtual memory in favor of residual memory.
+
+## 0.3.0
+
+  * FEAT: Introduction of global mz calibration.
+  * FEAT: Introduction of dia_cycle for diaPASEF.
+  * CHORE: Verified Python 3.9 compatibility.
+  * FEAT: Included option to open Bruker raw data when starting the GUI.
+  * FEAT: Provided hash for TimsTOF objects.
+  * FEAT: Filter push indices.
+  * CHORE: included stable and loose versions for all dependancies
+
+## 0.2.8
+
+  * FIX: Ensure stable version for one click GUI.
+  * FIX: Do not require plotting dependancies for CLI export csv selection.
+  * FIX: Import of very old diaPASEF samples where the analysis.tdf file still looks like ddaPASEF.
+  * FIX: frame pointers of fragment_frame table.
+  * FEAT: Include visual report in performance notebook.
+  * FEAT: Include DIA 120 sample in performance tests.
+  * FEAT: Show performance in README.
+  * FIX: Move python-lzf dependancy (to decompress older Bruker files) to legacy requirements, as pip install on Windows requires visual c++ otherwise.
+  * DOCS: BioRxiv paper link.
+  * FEAT/FIX: RT in min column.
+  * FEAT: CLI manual.
+  * FEAT: Inclusion of more coordinates in CLI.
+
+## 0.2.7
+
+  * CHORE: Introduction of changelog.
+  * CHORE: Automated publish_and_release action to parse version numbers.
+  * FEAT/FIX: Include average precursor mz in MGF titles and set unknown precursor charges to 0.
+  * FIX: Properly resolve set_global argument of `alphatims.utils.set_threads`.
+  * FIX: Set nogil option for `alphatims.bruker.indptr_lookup`.
+  * DOCS: GUI Manual typos.
+  * FEAT: Include buttons to download test data and citation in GUI.
+  * FEAT: Include option for progress_callback in alphatims.utils.pjit.
+  * FIX/FEAT: Older samples with TimsCompressionType 1 can now also be read. This is at limited performance.
+  * FEAT: By default use loose versioning for the base dependancies. Stable dependancy versions can be enforced with `pip install "alphatims[stable]"`. NOTE: This option is not guaranteed to be maintained. Future AlphaTims versions might opt for an intermediate solution with semi-strict dependancy versioning.

Dockerfile

@@ -1,22 +1,54 @@
+# syntax=docker/dockerfile:1
 
-# FROM python:3.9-slim
-FROM --platform=linux/amd64 python:3.9-bullseye
+FROM --platform=linux/amd64 python:3.9-bookworm
 
-RUN apt-get update && apt-get install -y build-essential gcc python3-dev
+# Prevents Python from writing pyc files.
+ENV PYTHONDONTWRITEBYTECODE=1
+# Keeps Python from buffering stdout and stderr to avoid situations where
+# the application crashes without emitting any logs due to buffering.
+ENV PYTHONUNBUFFERED=1
 
-RUN adduser worker
-USER worker
-WORKDIR /home/worker
+WORKDIR /app
 
-COPY --chown=worker:worker dist/*.whl /home/worker
 
-# RUN python3 -m pip install ".[plotting-stable]" # Image is 1.6gb with plotting
-# The size is reduced to 847 mb without it.
-RUN python3 -m pip install --disable-pip-version-check --no-cache-dir --user /home/worker/*.whl
-RUN ls /home/worker/.local/lib/python3.9/site-packages/alphatims/ext/timsdata.so
-RUN chmod 777 /home/worker/.local/lib/python3.9/site-packages/alphatims/ext/timsdata.so
+# Create a non-privileged user that the app will run under.
+# See https://docs.docker.com/go/dockerfile-user-best-practices/
+ARG UID=10001
+RUN adduser \
+    --disabled-password \
+    --gecos "" \
+    --home "/home/alphatimsuser" \
+    --shell "/sbin/nologin" \
+    --uid "${UID}" \
+    alphatimsuser
 
-RUN python3 -m pip cache purge
-ENV PATH="/home/worker/.local/bin:${PATH}"
+COPY requirements requirements
 
-ENTRYPOINT [ "alphatims" ]
+RUN pip install --no-cache-dir  -r requirements/requirements.txt
+RUN pip install --no-cache-dir  -r requirements/requirements_plotting.txt
+
+COPY alphatims alphatims
+COPY MANIFEST.in MANIFEST.in
+COPY LICENSE.txt LICENSE.txt
+COPY README.md README.md
+COPY pyproject.toml pyproject.toml
+
+RUN pip install --no-cache-dir ".[stable,plotting-stable]"
+
+RUN chmod 777 /usr/local/lib/python3.9/site-packages/alphatims/ext/timsdata.so
+RUN mkdir -p /usr/local/lib/python3.9/site-packages/alphatims/logs && chmod 777 /usr/local/lib/python3.9/site-packages/alphatims/logs
+
+ENV PORT=5006
+EXPOSE 5006
+
+# to allow other host ports than 5006
+ENV BOKEH_ALLOW_WS_ORIGIN=localhost
+
+USER alphatimsuser
+
+CMD ["/usr/local/bin/alphatims", "gui", "--port", "5006"]
+
+# build & run:
+# docker build --progress=plain -t alphatims .
+# DATA_FOLDER=/path/to/local/data
+# docker run -p 5006:5006 -v $DATA_FOLDER:/app/data/ -t alphatims