From b1b35e60a9ee2f34f49c287135c6bd98f9478316 Mon Sep 17 00:00:00 2001 From: Marten <58044494+McHaillet@users.noreply.github.com> Date: Tue, 27 Feb 2024 14:29:42 +0100 Subject: [PATCH 1/5] Update pyproject.toml --- pyproject.toml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 6dd9800d..f55d7b7a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,9 +3,9 @@ requires = ["setuptools"] build-backend = "setuptools.build_meta" [project] -name = "pytom-template-matching-gpu" +name = "pytom-match-pick" version = "0.3.5" -description = "GPU template matching from PyTOM as a lightweight pip package" +description = "PyTOM's GPU template matching module as an independent package" readme = "README.md" license = {file = "LICENSE"} authors = [ @@ -51,8 +51,8 @@ plotting = ["matplotlib", "seaborn"] "pytom_estimate_roc.py" = "pytom_tm.entry_points:estimate_roc [plotting]" [project.urls] -Repository = "https://github.com/SBC-Utrecht/pytom-template-matching-gpu" -Issues = "https://github.com/SBC-Utrecht/pytom-template-matching-gpu/issues" +Repository = "https://github.com/SBC-Utrecht/pytom-match-pick" +Issues = "https://github.com/SBC-Utrecht/pytom-match-pick/issues" [tool.setuptools] packages = ["pytom_tm", "pytom_tm.angle_lists"] From b0082b839c1a9d87aa8d68622fce4f54398f9127 Mon Sep 17 00:00:00 2001 From: Marten <58044494+McHaillet@users.noreply.github.com> Date: Tue, 27 Feb 2024 14:32:10 +0100 Subject: [PATCH 2/5] Update README.md --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 487423f0..1b46ab4a 100644 --- a/README.md +++ b/README.md @@ -39,8 +39,8 @@ conda activate pytom_tm Then clone the repository and install it with pip (building cupy can take a while!): ```commandline -git clone https://github.com/SBC-Utrecht/pytom-template-matching-gpu.git -cd pytom-template-matching-gpu +git clone https://github.com/SBC-Utrecht/pytom-match-pick.git +cd pytom-match-pick python -m pip install '.[plotting]' ``` @@ -73,9 +73,9 @@ specific build compatible with the installed cuda toolkit. ## Usage -Detailed usage instructions are available on the wiki: https://github.com/SBC-Utrecht/pytom-template-matching-gpu/wiki +Detailed usage instructions are available on the wiki: https://github.com/SBC-Utrecht/pytom-match-pick/wiki -Also, a tutorial can be found on the same wiki: https://github.com/SBC-Utrecht/pytom-template-matching-gpu/wiki/Tutorial +Also, a tutorial can be found on the same wiki: https://github.com/SBC-Utrecht/pytom-match-pick/wiki/Tutorial The following scripts are available to run with `--help` to see parameters: From 2301eb9e7a6590112b6b0163b76fcb29b17eeae0 Mon Sep 17 00:00:00 2001 From: Marten <58044494+McHaillet@users.noreply.github.com> Date: Tue, 27 Feb 2024 14:36:12 +0100 Subject: [PATCH 3/5] Update __init__.py --- src/pytom_tm/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pytom_tm/__init__.py b/src/pytom_tm/__init__.py index 22d3ec9e..bf84efe3 100644 --- a/src/pytom_tm/__init__.py +++ b/src/pytom_tm/__init__.py @@ -1,5 +1,5 @@ from importlib import metadata -__version__ = metadata.version('pytom-template-matching-gpu') +__version__ = metadata.version('pytom-match-pick') try: import cupy From 954a02107a8136c2ea211c6cff79befa364d36ee Mon Sep 17 00:00:00 2001 From: Marten <58044494+McHaillet@users.noreply.github.com> Date: Tue, 27 Feb 2024 14:42:22 +0100 Subject: [PATCH 4/5] get version from __init__ in tmjob --- src/pytom_tm/tmjob.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/pytom_tm/tmjob.py b/src/pytom_tm/tmjob.py index b71909b6..e4a2334c 100644 --- a/src/pytom_tm/tmjob.py +++ b/src/pytom_tm/tmjob.py @@ -14,6 +14,7 @@ from pytom_tm.matching import TemplateMatchingGPU from pytom_tm.weights import create_wedge, power_spectrum_profile, profile_to_weighting, create_gaussian_band_pass from pytom_tm.io import read_mrc_meta_data, read_mrc, write_mrc, UnequalSpacingError +from pytom_tm import __version__ as PYTOM_TM_VERSION def load_json_to_tmjob(file_name: pathlib.Path, load_for_extraction: bool = True) -> TMJob: @@ -101,7 +102,7 @@ def __init__( ctf_data: Optional[list[dict, ...]] = None, whiten_spectrum: bool = False, rotational_symmetry: int = 1, - pytom_tm_version_number: str = metadata.version('pytom-template-matching-gpu'), + pytom_tm_version_number: str = PYTOM_TM_VERSION, job_loaded_for_extraction: bool = False, ): """ From 68483dd61520ac802660ac7575ecf73dd93f67a7 Mon Sep 17 00:00:00 2001 From: Marten <58044494+McHaillet@users.noreply.github.com> Date: Tue, 27 Feb 2024 14:43:35 +0100 Subject: [PATCH 5/5] update badge in readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1b46ab4a..190b4638 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -![test-badge](https://github.com/SBC-Utrecht/pytom-template-matching-gpu/actions/workflows/unit-tests.yml/badge.svg?branch=main) +![test-badge](https://github.com/SBC-Utrecht/pytom-match-pick/actions/workflows/unit-tests.yml/badge.svg?branch=main) # PyTOM GPU template matching for cryo-ET PyTOM's GPU template matching as a single pip plugin that can only be run from the command line.