Merge branch 'build-2024.10.01' into 'staging'

Build 2024.10.01

See merge request rhodes/model_server!64

.gitignore

@@ -5,5 +5,6 @@
 
 # build and conda-build artifacts
 build/*
+conda-bld/*
 dist/*
 *.egg-info/*
\ No newline at end of file

.idea/.gitignore

-# Default ignored files
-/shelf/
-/workspace.xml

.idea/inspectionProfiles/profiles_settings.xml

-<component name="InspectionProjectProfileManager">
-  <settings>
-    <option name="USE_PROJECT_PROFILE" value="false" />
-    <version value="1.0" />
-  </settings>
-</component>
\ No newline at end of file

.idea/misc.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.9 (model_server_env)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file

.idea/model_server.iml

-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/model_server" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/tests" isTestSource="false" />
-    </content>
-    <orderEntry type="jdk" jdkName="Python 3.9 (model_server_env)" jdkType="Python SDK" />
-    <orderEntry type="sourceFolder" forTests="false" />
-  </component>
-</module>
\ No newline at end of file

.idea/modules.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/model_server.iml" filepath="$PROJECT_DIR$/.idea/model_server.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file

.idea/vcs.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="VcsDirectoryMappings">
-    <mapping directory="$PROJECT_DIR$" vcs="Git" />
-  </component>
-</project>
\ No newline at end of file

README.md

@@ -8,19 +8,29 @@ model_server is a service for on-demand computer vision, adapted specifically to
 and other life sciences applications.  It abstracts image data access, persists machine learning models, 
 and exposes an extensible API to facilitate low-latency analysis.  
 
-## Installation from source:
+## Install Git and miniforge
+1. Install Miniforge for environment management:<br>https://github.com/conda-forge/miniforge/releases
+2. Under the Start menu, open `Miniforge3 > Miniforge Prompt`
 
+## Option 1: install model_server as a package:
+1. Download the most recent version of the built package from:<br>https://git.embl.de/rhodes/model_server/-/packages/1280
+2. (optional) activate the target conda environment: `mamba activate <target_environment>`
+3. From the package repository https://git.embl.de/rhodes/model_server/-/packages/ download:
+   - The most recent requirements.yml
+   - The most recent .tar.bz2 file containing the built conda package
+4. In a text editor, open requirements.yml and remove all but the "channels" and "dependencies" blocks, then save.
+5. Change directories to the location of 'requirements.yml' and install dependencies:<br>`mamba env update -f requirements.yml`
+6. Download the most recent .tar.bz2 file containing the built conda package from:<br>https://git.embl.de/rhodes/model_server/-/packages/1283
+7. Change directories to the downloaded file and install model_server package: `mamba install model_server-<version>-py_0.tar.bz2`
+
+## Option 2: install model_server from source:
 1. Install Git:<br>https://git-scm.com/download/win
-2. Install Miniforge for environment management:<br>https://github.com/conda-forge/miniforge/releases
-3. Under the Start menu, open `Miniforge3 > Miniforge Prompt`
-4. In the new terminal, clone the model_server repository:<br>
-   `cd %userprofile%`<br>
-   `git clone https://almf-staff:KJmFvyPRbpzoVZDqfMzV@git.embl.de/rhodes/model_server.git`
-5. Create the environment: `mamba env create --file requirements.yml --name model_server_env`
-6. Activate the environment: `mamba activate model_server_env`
-7. Add the project source as a Python package: `pip install --no-deps -e .`
+2. In the new terminal, clone the model_server repository:<br>`cd %userprofile%`<br>`git clone https://almf-staff:KJmFvyPRbpzoVZDqfMzV@git.embl.de/rhodes/model_server.git`
+3. Create the target environment: `mamba env create --file requirements.yml --name model_server_env`
+4. Activate the target environment: `mamba activate model_server_env`
+5. Add the project source as a Python package: `pip install --no-deps -e .`
 
 ## To start the server:
-1. From the Miniforge prompt, run `mamba activate model_server_env`
+1. From the Miniforge prompt, run `mamba activate <target_environment>`
 2. Then run `python -m scripts.run_server --port 6221`
 3. A browser window should appear, with basic status information.

conda-recipe/publish.py

+"""
+Automate registration of conda build artifacts to EMBL GitLab;
+assumes API access token is recorded in ~/.pypirc shell configuration file
+"""
+from configparser import ConfigParser
+import json
+from pathlib import Path
+import requests
+
+id = '5668'
+proj = 'model_server'
+root = Path('../conda-bld/')
+
+# get authentication info from local config file
+cfg = ConfigParser()
+cfg.read(Path.home() / '.pypirc')
+user = cfg['gitlab-model-server']['username']
+pwd = cfg['gitlab-model-server']['password']
+
+with open(root / 'channeldata.json', 'r') as fh:
+    chdata = json.load(fh)
+
+# upload to GitLab API
+res = {}
+for sd in ['noarch', 'win-64']:
+    with open(root / sd / 'repodata.json', 'r') as fh:
+        dd = json.load(fh)
+    pkgname = f'conda_{sd}'
+
+    if len(dd['packages']) == 0:
+        continue
+
+    # put each .tar.bz2
+    for fn in dd['packages'].keys():
+        ver = dd['packages'][fn]['version']
+        stem = fn.split('.tar.bz2')[0]
+        res[(sd, fn)] = requests.put(
+            f'https://git.embl.de/api/v4/projects/{id}/packages/generic/{pkgname}/{ver}/{fn}?status=default',
+            files={'file': open(root / sd / fn, 'rb')},
+            headers={'PRIVATE-TOKEN': pwd},
+        )
+
+    # put requirements.yml
+    fn = 'requirements.yml'
+    res[(sd, fn)] = requests.put(
+        f'https://git.embl.de/api/v4/projects/{id}/packages/generic/{pkgname}/{ver}/{fn}?status=default',
+        files={'file': open(root.parent / fn, 'r')},
+        headers={'PRIVATE-TOKEN': pwd, 'Content-Type': 'text/html'},
+    )
+print('Finished')
+print(res)
\ No newline at end of file

requirements.yml

-name: model_server_mqtt
+name: model_server
 channels:
   - pytorch
   - ilastik-forge