From f33910bbec7e4db1a87016941e31d3ea4c412b17 Mon Sep 17 00:00:00 2001 From: Yuichi Motoyama Date: Tue, 5 Nov 2024 18:25:26 +0900 Subject: [PATCH 1/6] Drop a support of python 3.7/3.8 --- .github/workflows/Test_abICS.yml | 2 +- README.md | 12 ++++++------ docs/sphinx/en/source/install/install.rst | 2 +- docs/sphinx/ja/source/install/install.rst | 2 +- pyproject.toml | 3 +-- 5 files changed, 10 insertions(+), 11 deletions(-) diff --git a/.github/workflows/Test_abICS.yml b/.github/workflows/Test_abICS.yml index e67f2e47..44437bbd 100644 --- a/.github/workflows/Test_abICS.yml +++ b/.github/workflows/Test_abICS.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-20.04 strategy: matrix: - python-version: ['3.7', '3.8', '3.9', '3.10', '3.11'] + python-version: ['3.9', '3.12'] testname: [Unit, Sampling, ActiveLearn] fail-fast: false diff --git a/README.md b/README.md index 335761ce..f343ee39 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ and OpenMX input files for obtaining the reference training data for the machine ## Requirement -- python3 (>=3.7) +- python3 (>=3.9) - numpy - scipy - toml (for parsing input files) @@ -25,7 +25,7 @@ Pymatgen requires Cython but Cython will not be installed automatically, please make sure that this is installed, ``` bash -$ pip3 install Cython +$ python3 -m pip install Cython ``` mpi4py requires one of the MPI implementations such as OpenMPI, @@ -39,7 +39,7 @@ $ brew install open-mpi After installing Cython and MPI, ``` bash -$ pip3 install abics +$ python3 -m pip install abics ``` will install abICS and dependencies. @@ -48,10 +48,10 @@ If you want to change the directory where abICS is installed, add `--user` option or `--prefix=DIRECTORY` option to the above command as ``` bash -$ pip3 install --user abics +$ python3 -m pip install --user abics ``` -For details of `pip` , see the manual of `pip` by `pip3 help install` +For details of `pip` , see the manual of `pip` by `python3 -m pip help install` If you want to install abICS from source, see [wiki page](https://github.com/issp-center-dev/abICS/wiki/Install) @@ -93,6 +93,6 @@ Shusuke Kasamatsu, Yuichi Motoyama, Tatsumi Aoyama, Kazuyoshi Yoshimi [English online manual](https://issp-center-dev.github.io/abICS/docs/master/en/html/index.html) -[Japnese online manual](https://issp-center-dev.github.io/abICS/docs/master/ja/html/index.html) +[Japanese online manual](https://issp-center-dev.github.io/abICS/docs/master/ja/html/index.html) [API reference](https://issp-center-dev.github.io/abICS/docs/api/master/html/index.html) diff --git a/docs/sphinx/en/source/install/install.rst b/docs/sphinx/en/source/install/install.rst index 7f388b8e..7c10efa0 100644 --- a/docs/sphinx/en/source/install/install.rst +++ b/docs/sphinx/en/source/install/install.rst @@ -3,7 +3,7 @@ Prerequisites ~~~~~~~~~~~~~~~~~~~~~~ -abICS requires Python3 (>=3.7). +abICS requires Python3 (>=3.9). The following Python packages are required. diff --git a/docs/sphinx/ja/source/install/install.rst b/docs/sphinx/ja/source/install/install.rst index 73bbeebb..304bae71 100644 --- a/docs/sphinx/ja/source/install/install.rst +++ b/docs/sphinx/ja/source/install/install.rst @@ -3,7 +3,7 @@ 必要なライブラリ・環境 ~~~~~~~~~~~~~~~~~~~~~~ -abICS をインストール・実行するには、 バージョン3.7 以上の Python が必要です。 +abICS をインストール・実行するには、 バージョン3.9 以上の Python が必要です。 また、以下の Python パッケージが必要です。 - numpy diff --git a/pyproject.toml b/pyproject.toml index 233ba3cc..55cf18b4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,14 +13,13 @@ packages = [ ] [tool.poetry.dependencies] -python = "^3.7" +python = "^3.9" numpy = "^1.20" toml = ">=0.10" scipy = "^1" mpi4py = "^3" pymatgen = ">=2019.12.3 <2023.5.8" qe_tools = "^1.1" -"ruamel.yaml" = { version = "<0.18.0", python = "<3.8" } [tool.poetry.extras] From ec9aa15b9ca2b9162ac1a98ef68c0c637f87a377 Mon Sep 17 00:00:00 2001 From: Yuichi Motoyama Date: Tue, 5 Nov 2024 18:29:32 +0900 Subject: [PATCH 2/6] test with python 3.10 and 3.11 --- .github/workflows/Test_abICS.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/Test_abICS.yml b/.github/workflows/Test_abICS.yml index 44437bbd..14c3fdef 100644 --- a/.github/workflows/Test_abICS.yml +++ b/.github/workflows/Test_abICS.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-20.04 strategy: matrix: - python-version: ['3.9', '3.12'] + python-version: ['3.9', '3.10', '3.11'] testname: [Unit, Sampling, ActiveLearn] fail-fast: false From 7007069fd5baed4a12d7c2614dce0014b84f884e Mon Sep 17 00:00:00 2001 From: Yuichi Motoyama Date: Wed, 6 Nov 2024 16:08:05 +0900 Subject: [PATCH 3/6] update test --- tests/test_vasp.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/tests/test_vasp.py b/tests/test_vasp.py index 56eece29..f617f7ac 100644 --- a/tests/test_vasp.py +++ b/tests/test_vasp.py @@ -69,10 +69,8 @@ def test_input(self): self.assertEqual(res["INCAR"], ref["INCAR"]) self.assertTrue(res["POSCAR"].structure.matches(ref["POSCAR"].structure)) - self.assertEqual( - res["POSCAR"].structure.site_properties, - ref["POSCAR"].structure.site_properties, - ) + for k,v in ref["POSCAR"].structure.site_properties.items(): + self.assertTrue(np.allclose(res["POSCAR"].structure.site_properties[k], v)) def test_cl_algs(self): nprocs = 2 From 2623c16b56b81e3a822e856de35b1974f5930838 Mon Sep 17 00:00:00 2001 From: Yuichi Motoyama Date: Wed, 6 Nov 2024 16:12:19 +0900 Subject: [PATCH 4/6] fix conflict --- pyproject.toml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 00c3d8c3..71504b85 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,11 +20,7 @@ scipy = "^1" mpi4py = "^3" pymatgen = ">=2019.12.3 <2023.5.8" qe_tools = "^1.1" -<<<<<<< HEAD -======= nequip = {version=">=0.5.6", optional=true} -"ruamel.yaml" = { version = "<0.18.0", python = "<3.8" } ->>>>>>> develop [tool.poetry.extras] nequip = ["nequip"] From 91f0926b8e6e96b5bf896ed6c1042ed96a494cf1 Mon Sep 17 00:00:00 2001 From: Yuichi Motoyama Date: Wed, 6 Nov 2024 16:44:49 +0900 Subject: [PATCH 5/6] change pymatgen version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 71504b85..c068bba5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ numpy = "^1.20" toml = ">=0.10" scipy = "^1" mpi4py = "^3" -pymatgen = ">=2019.12.3 <2023.5.8" +pymatgen = ">=2022.1.20 <2023.5.8" qe_tools = "^1.1" nequip = {version=">=0.5.6", optional=true} From fc0f83edb75cfbc3f13c6fb635032678a9da86d9 Mon Sep 17 00:00:00 2001 From: Yuichi Motoyama Date: Wed, 6 Nov 2024 16:48:10 +0900 Subject: [PATCH 6/6] rm upper bound of pymatgen --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c068bba5..3c88cd1e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ numpy = "^1.20" toml = ">=0.10" scipy = "^1" mpi4py = "^3" -pymatgen = ">=2022.1.20 <2023.5.8" +pymatgen = ">=2022.1.20" qe_tools = "^1.1" nequip = {version=">=0.5.6", optional=true}