From 1e9e7c1fd1cc1b50e347773b7483324002294d38 Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.co.uk>
Date: Sun, 24 Mar 2024 08:44:09 +0000
Subject: [PATCH 1/6] Fix test

---
 src/alchemlyb/tests/test_workflow_ABFE.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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,

From 69861acd77f2d97b3950c4e4701e1b31a4bdcba3 Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.co.uk>
Date: Sun, 24 Mar 2024 09:34:06 +0000
Subject: [PATCH 2/6] fix ci

---
 .github/workflows/ci.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 0469f78f..89754ab3 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -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)

From 3f89a6ad94ea47eed1dc5d3b3108b248541078bd Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.co.uk>
Date: Sun, 24 Mar 2024 10:36:14 +0000
Subject: [PATCH 3/6] fixbalck

---
 src/alchemlyb/tests/parsing/test_amber.py          | 1 +
 src/alchemlyb/tests/parsing/test_namd.py           | 2 ++
 src/alchemlyb/tests/test_fep_estimators.py         | 1 +
 src/alchemlyb/tests/test_preprocessing.py          | 1 +
 src/alchemlyb/tests/test_ti_estimators.py          | 1 +
 src/alchemlyb/tests/test_ti_gaussian_quadrature.py | 1 +
 6 files changed, 7 insertions(+)

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

From 30b6c60e3ad78f2cc4bdee32e3a0046b5c304642 Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.co.uk>
Date: Sun, 24 Mar 2024 12:39:29 +0000
Subject: [PATCH 4/6] test new nest

---
 devtools/conda-envs/test_env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index a8795f1c..662527fa 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -24,5 +24,5 @@ dependencies:
 - sphinx_rtd_theme
 
 - pip:
-  - alchemtest @ https://github.com/alchemistry/alchemtest/archive/master.zip
+  - alchemtest @ git+https://github.com/xiki-tempula/alchemtest.git@feat_main
 

From 806d6114361acfbf70bf09f19c440069971b8a77 Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.co.uk>
Date: Sun, 31 Mar 2024 11:03:20 +0100
Subject: [PATCH 5/6] fix RTD

---
 .github/workflows/ci.yaml         | 2 +-
 devtools/conda-envs/test_env.yaml | 2 +-
 docs/requirements.yaml            | 9 +++++++++
 readthedocs.yml                   | 4 ++--
 4 files changed, 13 insertions(+), 4 deletions(-)
 create mode 100644 docs/requirements.yaml

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 89754ab3..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:
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 662527fa..a8795f1c 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -24,5 +24,5 @@ dependencies:
 - sphinx_rtd_theme
 
 - pip:
-  - alchemtest @ git+https://github.com/xiki-tempula/alchemtest.git@feat_main
+  - alchemtest @ https://github.com/alchemistry/alchemtest/archive/master.zip
 
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..4c77a2b4 100644
--- a/readthedocs.yml
+++ b/readthedocs.yml
@@ -13,9 +13,9 @@ build:
     python: "mambaforge-4.10"
 
 conda:
-    environment: devtools/conda-envs/test_env.yaml
+    environment: docs/requirements.yaml
 
 python:
   install:
     - method: pip
-      path: .
+      path: .
\ No newline at end of file

From ba3afe859559477cf0ef702b20ff30df1eb06543 Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.co.uk>
Date: Sun, 31 Mar 2024 11:08:03 +0100
Subject: [PATCH 6/6] add tailing line

---
 readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/readthedocs.yml b/readthedocs.yml
index 4c77a2b4..e053c3bc 100644
--- a/readthedocs.yml
+++ b/readthedocs.yml
@@ -18,4 +18,4 @@ conda:
 python:
   install:
     - method: pip
-      path: .
\ No newline at end of file
+      path: .