Update python version and fix testing issues (#329)

* use a stable url for testing

The BGC_GBK_URL changes from time to time

* update gnps website down function

* add condition of gnps website down for tests

* update python min version from 3.9 to 3.11

it is required by BigScape2

Author: CunliangGeng

.github/workflows/build.yml

@@ -30,15 +30,15 @@ on:
 jobs:
 
   smoke_test:
-    name: Smoke test on ubuntu for python 3.10
+    name: Smoke test on ubuntu for python 3.11
     runs-on: ubuntu-latest
     if: github.event.pull_request.draft == false
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v3
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: Python info
         shell: bash -l {0}
         run: |
@@ -64,7 +64,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest']
-        python-version: ['3.9', '3.11']
+        python-version: ['3.12']
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}

.github/workflows/deploy-docs.yml

@@ -23,7 +23,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
 
     - name: Install dependencies
       run: python3 -m pip install .[dev]

.github/workflows/format-typing-check.yml

@@ -30,10 +30,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v3
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: Install ruff and mypy
         run: |
           pip install ruff mypy typing_extensions \

.github/workflows/sonar-cloud.yml

@@ -43,7 +43,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: Install nplinker and its dependencies
         run: |
           python3 -m pip install -e .[dev]

README.dev.md

@@ -16,11 +16,11 @@ If you want to add more settings, you can update the workspace settings, see [th
 
 ## Setup
 
-We use Python 3.10 for development environment.
+We use Python 3.11 for development environment.
 
 ```shell
 # Create a virtual environment
-conda create -n npl-dev python=3.10
+conda create -n npl-dev python=3.11
 
 # activate virtual environment
 conda activate npl-dev
@@ -98,7 +98,7 @@ ruff format filename.py
 
 We use [inline type annotation](https://typing.readthedocs.io/en/latest/source/libraries.html#how-to-provide-type-annotations) for static typing rather than stub files (i.e. `.pyi` files).
 
-Since Python 3.10 is used as dev environment and NPLinker must support Python version ≥3.9, you may see various typing issues at runtime. Here is [a guide to solve the potential runtime issues](https://mypy.readthedocs.io/en/stable/runtime_troubles.html).
+Since Python 3.11 is used as dev environment (older NPLinker must support Python version ≥3.9), you may see various typing issues at runtime. Here is [a guide to solve the potential runtime issues](https://mypy.readthedocs.io/en/stable/runtime_troubles.html).
 
 By default, we use `from __future__ import annotations` at module level to stop evaluating annotations at function definition time (see [PEP 563](https://peps.python.org/pep-0563/)), which would solve most of compatibility issues between different Python versions. Make sure you're aware of the [caveats](https://mypy.readthedocs.io/en/stable/runtime_troubles.html#future-annotations-import-pep-563).
 

README.md

@@ -26,7 +26,7 @@ Original paper: [Ranking microbial metabolomic and genomic links in the NPLinker
 
 ### Requirement
 - Linux, MacOS or [Windows with WSL](https://learn.microsoft.com/en-us/windows/wsl/)
-- Python version ≥3.9
+- Python version ≥3.11
 
 
 ### Installation
@@ -35,8 +35,8 @@ requires <span style="color:red;">**~4.5GB**</span> of disk space to install all
 
 ```shell
 # Create a new virtual environment and activate it
-conda create -n npl-3.10 python=3.10
-conda activate npl-3.10 
+conda create -n npl-3.11 python=3.11
+conda activate npl-3.11 
 
 # install from nplinker releases (requiring ~300MB of disk space)
 pip install --pre nplinker
@@ -51,8 +51,8 @@ To run the tests, you need to clone this repo and install the development depend
 
 ```shell
 # Create a new virtual environment
-conda create -n npl-3.10 python=3.10
-conda activate npl-3.10
+conda create -n npl-3.11 python=3.11
+conda activate npl-3.11
 
 # Clone the repository and install the development dependencies
 git clone https://github.com/NPLinker/nplinker.git

docs/install.md

@@ -1,7 +1,7 @@
 
 !!!- Note "Requirements"
     - Linux, MacOS or [Windows with WSL](https://learn.microsoft.com/en-us/windows/wsl/)
-    - Python version ≥3.9
+    - Python version ≥3.11
 
 
 NPLinker is a python package that has both pypi packages and non-pypi packages as dependencies. It 
@@ -11,8 +11,8 @@ Install `nplinker` package as following:
 
 ```bash title="Install nplinker package"
 # Create a new virtual environment and activate it
-conda create -n npl-3.10 python=3.10  # (1)!
-conda activate npl-3.10 
+conda create -n npl-3.11 python=3.11  # (1)!
+conda activate npl-3.11 
 
 # install nplinker package (requiring ~300MB of disk space)
 pip install --pre nplinker # (2)!

docs/webapp/readme.md

@@ -85,8 +85,8 @@ Follow these steps to install the application directly on your system:
 
 2. **Set up a conda environment**
    ```bash
-    # Create a new conda environment with Python 3.10
-    conda create -n nplinker-webapp python=3.10
+    # Create a new conda environment with Python 3.11
+    conda create -n nplinker-webapp python=3.11
 
     # Activate the environment
     conda activate nplinker-webapp
@@ -113,7 +113,7 @@ Follow these steps to install the application directly on your system:
 
 <ul>
   <li><strong>Port already in use</strong>: If port 8050 is already in use, modify the port in <code>app/main.py</code> by changing <code>app.run_server(debug=True, port=8050)</code></li>
-  <li><strong>Package installation errors</strong>: Make sure you're using Python 3.10 and that your pip is up-to-date</li>
+  <li><strong>Package installation errors</strong>: Make sure you're using Python 3.11 and that your pip is up-to-date</li>
 </ul>
 
 <p>If you encounter other problems, please check the <a href="https://github.com/NPLinker/nplinker-webapp/issues">Issues</a> page or create a new issue.</p>

pyproject.toml

@@ -9,7 +9,7 @@ name = "nplinker"
 version = "2.0.0-alpha.9"
 description = "Natural Products Linker"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.11"
 keywords = ["Genome", "Metabolome", "Natural Products", "Data Mining"]
 license = { text = "Apache-2.0 license" }
 classifiers = [
@@ -21,8 +21,6 @@ classifiers = [
     "Operating System :: MacOS",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
 ]
@@ -102,13 +100,13 @@ relative_files = true # show relative path in report, important for sonarcloud
 # Mypy: to check static type
 # see https://mypy.readthedocs.io/en/stable/config_file.html#example-pyproject-toml
 [tool.mypy]
-python_version = "3.10"
+python_version = "3.11"
 warn_return_any = true
 warn_unused_configs = true
 ignore_missing_imports = true
 
 [tool.ruff]
-target-version = "py310"
+target-version = "py311"
 line-length = 100
 
 [tool.ruff.lint]

setup.py

@@ -3,7 +3,7 @@
 from setuptools import setup
 
 
-if sys.version_info[:2] < (3, 9):
-    raise RuntimeError("Python version >= 3.9 required.")
+if sys.version_info[:2] < (3, 11):
+    raise RuntimeError("Python version >= 3.11 required.")
 
 setup(scripts=["bin/install-nplinker-deps"])