Merge branch 'master' into 347-docs-clarification-relating-to-matrix

.github/workflows/ci.yaml

@@ -29,7 +29,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macOS-latest", "windows-latest"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11"]
         # Only test lowest and highest version on the expensive/slow
         # macOS and windows runners (UPDATE when supported versions change):	
         exclude:
@@ -50,7 +50,7 @@ jobs:
       with:
         environment-file: devtools/conda-envs/test_env.yaml
         environment-name: test
-        extra-specs: |
+        create-args: |
             python=${{ matrix.python-version }}
 
     - name: Install package (with no dependencies)

docs/requirements.yaml

@@ -0,0 +1,9 @@
+name: docs
+channels:
+dependencies:
+    # Base depends
+  - python=3.10
+  - pip
+  # Doc
+  - sphinx
+  - sphinx_rtd_theme

readthedocs.yml

@@ -13,7 +13,7 @@ build:
     python: "mambaforge-4.10"
 
 conda:
-    environment: devtools/conda-envs/test_env.yaml
+    environment: docs/requirements.yaml
 
 python:
   install:

src/alchemlyb/tests/parsing/test_amber.py

@@ -1,6 +1,7 @@
 """Amber parser tests.
 
 """
+
 import bz2
 import logging
 

src/alchemlyb/tests/parsing/test_namd.py

@@ -1,6 +1,7 @@
 """NAMD parser tests.
 
 """
+
 import bz2
 from os.path import basename
 from re import search
@@ -13,6 +14,7 @@
 
 from alchemlyb.parsing.namd import extract_u_nk, extract
 
+
 # Indices of lambda values in the following line in NAMD fepout files:
 # #NEW FEP WINDOW: LAMBDA SET TO 0.6 LAMBDA2 0.7 LAMBDA_IDWS 0.5
 LAMBDA1_IDX_NEW = 6

src/alchemlyb/tests/test_fep_estimators.py

@@ -1,6 +1,7 @@
 """Tests for all FEP-based estimators in ``alchemlyb``.
 
 """
+
 import pytest
 
 import alchemlyb

src/alchemlyb/tests/test_preprocessing.py

@@ -1,6 +1,7 @@
 """Tests for preprocessing functions.
 
 """
+
 import logging
 
 import numpy as np

src/alchemlyb/tests/test_ti_estimators.py

@@ -1,6 +1,7 @@
 """Tests for all TI-based estimators in ``alchemlyb``.
 
 """
+
 import pandas as pd
 import pytest
 

src/alchemlyb/tests/test_ti_gaussian_quadrature.py

@@ -1,6 +1,7 @@
 """Tests for all TI-based estimators in ``alchemlyb``.
 
 """
+
 import pandas as pd
 import numpy as np
 import copy

src/alchemlyb/tests/test_workflow_ABFE.py

@@ -35,10 +35,10 @@ def workflow(tmp_path_factory):
 
 
 class TestInit:
-    def test_nofilematch(self):
+    def test_nofilematch(self, tmp_path):
         with pytest.raises(ValueError, match="No file has been matched to"):
             ABFE(
-                dir="./",
+                dir=str(tmp_path),
                 prefix="dhdl",
                 suffix="xvg",
                 T=310,