diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 0469f78f..6c666e99 100644 --- a/.github/workflows/ci.yaml +++ b/.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) diff --git a/docs/requirements.yaml b/docs/requirements.yaml new file mode 100644 index 00000000..c008b03e --- /dev/null +++ b/docs/requirements.yaml @@ -0,0 +1,9 @@ +name: docs +channels: +dependencies: + # Base depends + - python=3.10 + - pip + # Doc + - sphinx + - sphinx_rtd_theme diff --git a/readthedocs.yml b/readthedocs.yml index 0c61d50f..e053c3bc 100644 --- a/readthedocs.yml +++ b/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: diff --git a/src/alchemlyb/tests/parsing/test_amber.py b/src/alchemlyb/tests/parsing/test_amber.py index 21b6064e..b74cab4b 100644 --- a/src/alchemlyb/tests/parsing/test_amber.py +++ b/src/alchemlyb/tests/parsing/test_amber.py @@ -1,6 +1,7 @@ """Amber parser tests. """ + import bz2 import logging diff --git a/src/alchemlyb/tests/parsing/test_namd.py b/src/alchemlyb/tests/parsing/test_namd.py index f5168e8f..e3f5ea7c 100644 --- a/src/alchemlyb/tests/parsing/test_namd.py +++ b/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 diff --git a/src/alchemlyb/tests/test_fep_estimators.py b/src/alchemlyb/tests/test_fep_estimators.py index 03d0122f..a956dbbc 100644 --- a/src/alchemlyb/tests/test_fep_estimators.py +++ b/src/alchemlyb/tests/test_fep_estimators.py @@ -1,6 +1,7 @@ """Tests for all FEP-based estimators in ``alchemlyb``. """ + import pytest import alchemlyb diff --git a/src/alchemlyb/tests/test_preprocessing.py b/src/alchemlyb/tests/test_preprocessing.py index d64c7267..2ce7677c 100644 --- a/src/alchemlyb/tests/test_preprocessing.py +++ b/src/alchemlyb/tests/test_preprocessing.py @@ -1,6 +1,7 @@ """Tests for preprocessing functions. """ + import logging import numpy as np diff --git a/src/alchemlyb/tests/test_ti_estimators.py b/src/alchemlyb/tests/test_ti_estimators.py index 5c644547..3fc490f4 100644 --- a/src/alchemlyb/tests/test_ti_estimators.py +++ b/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 diff --git a/src/alchemlyb/tests/test_ti_gaussian_quadrature.py b/src/alchemlyb/tests/test_ti_gaussian_quadrature.py index 2e331409..d3f772fd 100644 --- a/src/alchemlyb/tests/test_ti_gaussian_quadrature.py +++ b/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 diff --git a/src/alchemlyb/tests/test_workflow_ABFE.py b/src/alchemlyb/tests/test_workflow_ABFE.py index c2dc4b15..0177f292 100644 --- a/src/alchemlyb/tests/test_workflow_ABFE.py +++ b/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,