From 9669672655b535aa0a52021baec3a3f735d01441 Mon Sep 17 00:00:00 2001 From: Yutack Park <111348843+YutackPark@users.noreply.github.com> Date: Tue, 26 Nov 2024 10:58:42 +0900 Subject: [PATCH 1/5] docs: update `sevenn_graph_build` of README.md --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 3fde3ce..156f9ce 100644 --- a/README.md +++ b/README.md @@ -148,7 +148,10 @@ Please note that `batch_size` in input.yaml indicates `batch_size` per GPU. sevenn_graph_build my_train_data.extxyz 5.0 ``` -You can preprocess the dataset with `sevenn_graph_build` to obtain `*.sevenn_data` files. The cutoff length should be provided. +You can preprocess the dataset with `sevenn_graph_build` to obtain `./sevenn_data/graph.pt` files. They can be used for training (`sevenn`) or +inference (`sevenn_inference`), skipping graph build stage. `./sevenn_data/graph.yaml` contains statistics and meta information for the dataset. +Those files must be located under the `sevenn_data`. If you move the dataset, move the whole `sevenn_data` directory, without changing the contents. + See `sevenn_graph_build --help` for more information. ### sevenn_inference From 3e7a4fb3e4a953fdaa9c39ee8b66dd08b117b17b Mon Sep 17 00:00:00 2001 From: Yutack Park <111348843+YutackPark@users.noreply.github.com> Date: Tue, 26 Nov 2024 11:01:01 +0900 Subject: [PATCH 2/5] docs: grammar --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 156f9ce..7028e3f 100644 --- a/README.md +++ b/README.md @@ -148,9 +148,9 @@ Please note that `batch_size` in input.yaml indicates `batch_size` per GPU. sevenn_graph_build my_train_data.extxyz 5.0 ``` -You can preprocess the dataset with `sevenn_graph_build` to obtain `./sevenn_data/graph.pt` files. They can be used for training (`sevenn`) or -inference (`sevenn_inference`), skipping graph build stage. `./sevenn_data/graph.yaml` contains statistics and meta information for the dataset. -Those files must be located under the `sevenn_data`. If you move the dataset, move the whole `sevenn_data` directory, without changing the contents. +You can preprocess the dataset with `sevenn_graph_build` to obtain `./sevenn_data/graph.pt` files. These files can be used for training (`sevenn`) or +inference (`sevenn_inference`), skipping the graph build stage. `./sevenn_data/graph.yaml` contains statistics and meta information for the dataset. +These files must be located under the `sevenn_data`. If you move the dataset, move the entire `sevenn_data` directory without changing the contents. See `sevenn_graph_build --help` for more information. From 458c8f78ef22cb98df636d4a5a7d290394f3aece Mon Sep 17 00:00:00 2001 From: YutackPark Date: Tue, 26 Nov 2024 11:06:07 +0900 Subject: [PATCH 3/5] docs: 0.10.2 && add haekwan author info --- pyproject.toml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index cc87feb..f34f6ea 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,9 @@ [project] name = "sevenn" -version = "0.10.2.dev" +version = "0.10.2" authors = [ { name = "Yutack Park", email = "parkyutack@snu.ac.kr" }, + { name = "Haekwan Jeon", email = "haekwan98@snu.ac.kr" }, { name = "Jaesun Kim" }, { name = "Gijin Kim" }, { name = "Hyungmin An" }, @@ -28,7 +29,7 @@ dependencies = [ #"matscipy", ] [project.optional-dependencies] -matscipy = ["matscipy"] +opt = ["matscipy"] [project.scripts] From 59776e21274956151e5339ba78054bed5b13ea68 Mon Sep 17 00:00:00 2001 From: YutackPark Date: Tue, 26 Nov 2024 20:32:41 +0900 Subject: [PATCH 4/5] chore: add matscipy and pytest for test optonals --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index f34f6ea..1f48830 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,6 +29,7 @@ dependencies = [ #"matscipy", ] [project.optional-dependencies] +test = ["matscipy", "pytest-cov>=5"] opt = ["matscipy"] From 70a3ef0a633efa462ebe9ddecbb1ff6d682904c3 Mon Sep 17 00:00:00 2001 From: YutackPark Date: Wed, 27 Nov 2024 22:24:18 +0900 Subject: [PATCH 5/5] add matscipy as dependency --- CHANGELOG.md | 2 ++ pyproject.toml | 3 +-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ce80a1c..d118e74 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ All notable changes to this project will be documented in this file. ## [0.10.2] ### Added - Accelerated graph build routine if matscipy is installed @hexagonerose +### Changed +- matscipy is included as dependency ## [0.10.1] ### Added diff --git a/pyproject.toml b/pyproject.toml index 1f48830..56cfa77 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,11 +26,10 @@ dependencies = [ "scikit-learn", "torch_geometric>=2.5.0", "numpy<2.0", - #"matscipy", + "matscipy", ] [project.optional-dependencies] test = ["matscipy", "pytest-cov>=5"] -opt = ["matscipy"] [project.scripts]