Merge pull request #271 from iBridges-for-iRods/develop

Small updates for v1.1.1

.github/workflows/integration-tests-irods.yml

@@ -4,7 +4,15 @@ on:
   push:
     branches:
       - develop
+    paths-ignore:
+      - 'docs/**'
+      - 'tutorials/**'
+      - 'README.md'
   pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - 'tutorials/**'
+      - 'README.md'
 
 jobs:
   build:

.github/workflows/integration-tests-yoda.yml

@@ -4,7 +4,15 @@ on:
   push:
     branches:
       - develop
+    paths-ignore:
+      - 'docs/**'
+      - 'tutorials/**'
+      - 'README.md'
   pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - 'tutorials/**'
+      - 'README.md'
 
 jobs:
   build:

.github/workflows/main.yml

@@ -15,47 +15,76 @@ on:
 jobs:
   build:
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         os: [ubuntu-latest]
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         include:
           - os: windows-latest
-            python-version: "3.11"
+            python-version: "3.12"
           - os: macos-latest
-            python-version: "3.11"
+            python-version: "3.12"
     runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Clone the repository
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install ".[test]"
+
+      - name: Test with pytest
+        run: |
+          pytest tests
+          
+      - name: Lint with PyLint
+        run: |
+          pylint ibridges
+          
+      - name: Check types with MyPy
+        run: |
+          mypy ibridges
+
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
 
+      - name: Set up Python
+        uses: actions/setup-python@v4
+
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install ".[test]"
+
+      - name: Lint with Ruff
+        run: |
+          ruff check ibridges
+
+
+  docs:
+    runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install .[test]
-
-    - name: Lint with Ruff
-      run: |
-        ruff check ibridges
-
-    - name: Lint with PyLint
-      run: |
-        pylint ibridges
-
-    - name: Check types with MyPy
-      run: |
-        mypy ibridges
-
-    - name: Check if documentation builds.
-      run: |
-        cd docs; make html SPHINXOPTS="--keep-going"
-
-    - name: Test with pytest
-      run: |
-        pip install pytest
-        pytest tests
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: |
+          pip install ".[docs]"
+
+      - name: Check if documentation builds.
+        run: |
+          cd docs; make html SPHINXOPTS="--keep-going"

.gitignore

@@ -4,6 +4,7 @@ irods-basicGUI/logs/*
 irods-iBridgesGui.spec
 *DS_Store
 docs/source/api/generated
+docs/outputdir
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

.readthedocs.yaml

@@ -10,18 +10,15 @@ build:
   os: ubuntu-20.04
   tools:
     python: "3.9"
-    # You can also specify other tool versions:
-    # nodejs: "16"
-    # rust: "1.55"
-    # golang: "1.17"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/source/conf.py
+  configuration: docs/source/conf.py
 
 # Optionally declare the Python requirements required to build your docs
 python:
-   install:
-   - requirements: docs/requirements.txt
-   - method: pip
-     path: .
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

README.md

@@ -1,9 +1,11 @@
-# iBridges <img src="docs/logo.png" width="150" align="right">
+# iBridges <img src="https://github.com/iBridges-for-iRods/iBridges/blob/main/docs/logo.png?raw=true" width="150" align="right">
 iBridges is a library for scientific programmers who are working with data in iRODS. We provide a wrapper around the [python-irodsclient](https://pypi.org/project/python-irodsclient/) to facilitate easy interaction with the iRODS server. iBridges is currently still in very active development.
 
 [![PyPI version](https://badge.fury.io/py/ibridges.svg)](https://badge.fury.io/py/ibridges)
-[![](https://github.com/UtrechtUniversity/iBridges/actions/workflows/integration-tests-irods.yml/badge.svg?branch=develop)](https://github.com/UtrechtUniversity/iBridges/actions/workflows/integration-tests-irods.yml) [![](https://github.com/UtrechtUniversity/iBridges/actions/workflows/main.yml/badge.svg?branch=develop)](https://github.com/UtrechtUniversity/iBridges/actions/workflows/main.yml) 
-[![](https://github.com/UtrechtUniversity/iBridges/actions/workflows/integration-tests-yoda.yml/badge.svg)](https://github.com/UtrechtUniversity/iBridges/actions/workflows/integration-tests-yoda.yml) ![](https://readthedocs.org/projects/ibridges/badge/?version=latest&style=flat-default)
+[![Run integration tests against iRODS](https://github.com/iBridges-for-iRods/iBridges/actions/workflows/integration-tests-irods.yml/badge.svg)](https://github.com/iBridges-for-iRods/iBridges/actions/workflows/integration-tests-irods.yml)
+[![Run integration tests against Yoda](https://github.com/iBridges-for-iRods/iBridges/actions/workflows/integration-tests-yoda.yml/badge.svg)](https://github.com/iBridges-for-iRods/iBridges/actions/workflows/integration-tests-yoda.yml)
+[![Python package](https://github.com/iBridges-for-iRods/iBridges/actions/workflows/main.yml/badge.svg)](https://github.com/iBridges-for-iRods/iBridges/actions/workflows/main.yml)
+![](https://readthedocs.org/projects/ibridges/badge/?version=latest&style=flat-default)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12583187.svg)](https://doi.org/10.5281/zenodo.12583187)
 
 ## Highlights
@@ -20,17 +22,18 @@ iBridges is a library for scientific programmers who are working with data in iR
 - Small number of dependencies (`python-irodsclient` and `tqdm`)
 - Safe default options when working with your data.
 
+**iBridges** also has a graphical user interface, which you can install [here](https://github.com/iBridges-for-iRods/iBridges-GUI).
 
  <p align="center">
-    <a href="https://github.com/UtrechtUniversity/iBridges/issues/new?assignees=&labels=&projects=&template=bug_report.md&title=%5BBUG%5D">Report Bug</a>
+    <a href="https://github.com/iBridges-for-iRods/iBridges/issues/new?assignees=&labels=&projects=&template=bug_report.md&title=%5BBUG%5D">Report Bug</a>
     .
-    <a href="https://github.com/UtrechtUniversity/iBridges/issues/new?assignees=&labels=&projects=&template=feature_request.md&title=%5BFEATURE%5D">Request Feature</a>
+    <a href="https://github.com/iBridges-for-iRods/iBridges/issues/new?assignees=&labels=&projects=&template=feature_request.md&title=%5BFEATURE%5D">Request Feature</a>
     .
-    <a href="https://github.com/UtrechtUniversity/iBridges/discussions/categories/ideas">Share an idea</a>
+    <a href="https://github.com/iBridges-for-iRods/iBridges/discussions/categories/ideas">Share an idea</a>
     .
-    <a href="https://github.com/UtrechtUniversity/iBridges/discussions/categories/general">Leave some feedback</a>
+    <a href="https://github.com/iBridges-for-iRods/iBridges/discussions/categories/general">Leave some feedback</a>
     .
-    <a href="https://github.com/UtrechtUniversity/iBridges/discussions/categories/q-a">Ask a question</a>
+    <a href="https://github.com/iBridges-for-iRods/iBridges/discussions/categories/q-a">Ask a question</a>
   </p>
 </p>
 
@@ -45,7 +48,7 @@ pip install ibridges
 If you want to install the unstable version to test out new features, you can install the development branch:
 
 ```bash
-pip install git+https://github.com/UtrechtUniversity/iBridges.git@develop
+pip install git+https://github.com/iBridges-for-iRods/iBridges.git@develop
 ```
 
 ## Configuration

docker/irods_catalog_provider/Dockerfile

@@ -1,33 +1,46 @@
 FROM ubuntu:22.04
-ARG os_name=jammy
 
 ENV DEBIAN_FRONTEND=noninteractive
-ARG ubuntu_name=focal
 
-RUN apt-get update
-RUN apt-get install -y lsb-release gnupg wget sudo
-RUN apt-get clean && \
+RUN apt-get update && \
+    apt-get install -y \
+        apt-transport-https \
+        gnupg \
+        wget \
+    && \
+    apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/*
 
-# IRODS SERVER PACKAGES
-RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
-RUN sudo rm -rf /etc/apt/sources.list.d/renci-irods.list
-RUN sudo echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" |sudo tee /etc/apt/sources.list.d/renci-irods.list
+RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
+    echo "deb [arch=amd64] https://packages.irods.org/apt/ jammy main" | tee /etc/apt/sources.list.d/renci-irods.list
 
-RUN apt-get update
-RUN apt-get install -y python3 unixodbc
-RUN apt-get clean && \
+RUN apt-get update && \
+    apt-get install -y \
+        libcurl4-gnutls-dev \
+        python3 \
+        python3-distro \
+        python3-jsonschema \
+        python3-pip \
+        python3-psutil \
+        python3-requests \
+        rsyslog \
+        unixodbc \
+    && \
+    apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/*
 
-ARG irods_version=4.3.2
-ARG irods_package_version_suffix=-0~${os_name}
+ARG irods_version=4.3.3
+ARG irods_package_version_suffix=-0~jammy
 ARG irods_package_version=${irods_version}${irods_package_version_suffix}
-#ARG irods_resource_plugin_version=${irods_version}.0${irods_package_version_suffix}
+ARG irods_package_plugin_version_suffix=-0+${irods_version}~jammy
 
 RUN apt-get update && \
-    apt-get install -y irods-database-plugin-postgres=$irods_package_version
-RUN apt-get install irods-server=$irods_package_version
-RUN apt-get clean && \
+    apt-get install -y \
+        irods-database-plugin-postgres=${irods_package_version} \
+        irods-runtime=${irods_package_version} \
+        irods-server=${irods_package_version} \
+    && \
+    apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/*
 
 COPY setup-${irods_version}.input /

docker/irods_catalog_provider/setup-4.3.3.input

@@ -0,0 +1,29 @@
+
+
+
+
+irods-catalog
+5432
+ICAT
+irods
+y
+testpassword
+
+y
+demoResc
+
+tempZone
+1247
+20000
+20199
+1248
+
+rods
+y
+TEMPORARY_ZONE_KEY
+32_byte_server_negotiation_key__
+32_byte_server_control_plane_key
+rods
+
+
+

docker/irods_client/environments/plain-irods/config.toml

@@ -1,5 +1,5 @@
 password = "rods"
-server_version = "4.3.2"
+server_version = "4.3.3"
 can_write_pam_pass = false
 has_cached_pw = true
 resources = ["demoResc", "resc2"]

docs/source/data_transfers.rst

@@ -13,7 +13,7 @@ collections, :meth:`IrodsPath.create_collection` can be used.
 .. note::
     By default, no data will be overwritten. If you want to overwrite data, you
     can set :code:`overwrite=True`. Beware that you can also overwrite newer data with older data this way.
-    If a file and a dataobject are exactly the same, iBridges will silently skip the transfer,
+    If a file and a dataobject are exactly the same, iBridges will skip the transfer and print a warning,
     thereby saving time.
 
 For all operations, iBridges will check that the transfer has been completed without
@@ -34,7 +34,7 @@ If the transfer concerned a folder, a new collection with the folder name will b
     from ibridges import IrodsPath
     from pathlib import Path
  
-    local_path = Path("/path/to the/data/to/upload")
+    local_path = Path("/path/to/the/data/to/upload")
     irods_path = IrodsPath(session, '~', 'new_coll')
     upload(session, local_path, irods_path)
 
@@ -114,13 +114,12 @@ With the `python-irodsclient` which `iBridges` is built on, we can open the file
 That works without any problems for textual data. 
 
 .. code-block:: python
-  
+
     from ibridges import IrodsPath
-  
-  	obj_path = IrodsPath(session, "path", "to", "object")
-  	
-  	with obj_path.open('r') as stream:
-  	    content = stream.read().decode()
+
+    obj_path = IrodsPath(session, "path", "to", "object")
+    with obj_path.open('r') as stream:
+        content = stream.read().decode()
 	
 	
 Some python libraries allow to be instantiated directly from such a stream. This is supported by e.g. `pandas`, `polars` and `whisper`.
@@ -129,6 +128,7 @@ Some python libraries allow to be instantiated directly from such a stream. This
 
     import pandas as pd
 
-	with obj_path.open('r') as stream:
-		df = pd.read_csv(stream)
-	print(df)
+    with obj_path.open('r') as stream:
+        df = pd.read_csv(stream)
+	
+    print(df)