From f6f615c7228d015ce91200c8eb7d7c68333cd1bf Mon Sep 17 00:00:00 2001
From: IAlibay <ialibay@mdanalysis.org>
Date: Sun, 21 Jul 2024 21:53:30 -0400
Subject: [PATCH] fix ci, bump up python to 3.10+

---
 .github/workflows/gh-ci.yaml | 38 +++++++++++-------------------------
 CHANGELOG.md                 |  8 ++++++++
 build.sh                     |  3 ---
 meta.yaml                    | 20 -------------------
 pyproject.toml               |  5 ++---
 5 files changed, 21 insertions(+), 53 deletions(-)
 delete mode 100644 build.sh
 delete mode 100644 meta.yaml

diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
index ead7dd9..e67b1ac 100644
--- a/.github/workflows/gh-ci.yaml
+++ b/.github/workflows/gh-ci.yaml
@@ -23,31 +23,18 @@ defaults:
     shell: bash  -l {0} 
 
 jobs:
-  environment-config:
-    runs-on: ubuntu-latest
-    outputs:
-      stable-python-version: ${{ steps.get-python-version.outputs.python-version }}
-    steps:
-      - uses: actions/checkout@v4
-
-      - id: get-python-version
-        uses: MDAnalysis/get-latest-python-version@main
-        with:
-          last-n-minor-release: 1
-
   main-tests:
     if: "github.repository == 'MDAnalysis/mdahole2'"
     runs-on: ${{ matrix.os }}
     strategy:
         fail-fast: false
         matrix:
-          # os: [macOS-latest, ubuntu-latest, windows-latest]
-          os: [ubuntu-latest, macOS-latest]
-          python-version: ["3.9", "3.10", "3.11", "3.12"]
+          os: [ubuntu-latest, macos-latest, macos-13]
+          python-version: ["3.10", "3.11", "3.12"]
           mdanalysis-version: ["latest", "develop"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Build information
       run: |
@@ -58,12 +45,11 @@ jobs:
 
     # More info on options: https://github.com/conda-incubator/setup-miniconda
     - name: Install conda dependencies
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/conda-envs/test_env.yaml
         add-pip-as-python-dependency: true
-        architecture: x64
 
         miniforge-variant: Mambaforge
         use-mamba: true
@@ -101,10 +87,10 @@ jobs:
       env:
         DUECREDIT_ENABLE: 'yes'
       run: |
-        pytest -n 2 -v --cov=mdahole2 --cov-report=xml --color=yes mdahole2/tests/
+        pytest -n auto -v --cov=mdahole2 --cov-report=xml --color=yes mdahole2/tests/
 
     - name: codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.xml
@@ -114,16 +100,15 @@ jobs:
 
   pylint_check:
     if: "github.repository == 'MDAnalysis/mdahole2'"
-    needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: ${{ needs.environment-config.outputs.stable-python-version }}
+        python-version: "3.11"
 
     - name: Install Pylint
       run: |
@@ -140,16 +125,15 @@ jobs:
 
   pypi_check:
     if: "github.repository == 'MDAnalysis/mdahole2'"
-    needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }}
-      uses: actions/setup-python@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        python-version: ${{ needs.environment-config.outputs.stable-python-version }}
+        python-version: "3.11"
 
     - name: Install dependencies
       run: |
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a8e3d90..5c47b4d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,14 @@ The rules for this file:
   * accompany each entry with github issue/PR number (Issue #xyz)
 -->
 
+## Unreleased
+
+### Authors
+- IAlibay
+
+## Changed
+- Python 3.9 has now been dropped as per SPEC0
+
 ## [0.4.0] -- 2024-01-30
 
 ### Authors
diff --git a/build.sh b/build.sh
deleted file mode 100644
index 595a1c1..0000000
--- a/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/usr/bin/env bash
-
-pip install . --no-deps
diff --git a/meta.yaml b/meta.yaml
deleted file mode 100644
index cfb448d..0000000
--- a/meta.yaml
+++ /dev/null
@@ -1,20 +0,0 @@
-package:
-  name: mdahole2
-  version: "0.2.0"
-
-source:
-  path: .
-  
-requirements:
-  channels:
-    - conda-forge
-    - defaults
-  
-  build:
-    - python
-    - setuptools
-
-  run:
-    - python
-    - hole2
-    - mdanalysis
diff --git a/pyproject.toml b/pyproject.toml
index 49473bd..3898295 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,7 +22,6 @@ classifiers = [
     "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
     "Programming Language :: C",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -30,9 +29,9 @@ classifiers = [
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
-    "MDAnalysis>=2.0.0",
+    "MDAnalysis>=2.1.0",
 ]
 keywords = [
     "molecular simulations",