From fd5184f0ab67774507dc517769e196065fc4f43b Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Wed, 31 Aug 2022 14:07:50 -0700 Subject: [PATCH 1/7] update readme install instructions --- README.md | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index cf65624a4..4df4f2e47 100644 --- a/README.md +++ b/README.md @@ -6,19 +6,16 @@ algorithm to pack molecular recipes +### Prerequisite +1. Install Conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html ### Setup 1. create a virtual env: `conda create -n autopack` -2. `activate autopack` +2. `conda activate autopack` 3. `pip install -e .[dev]` -### Run analysis code -By default analyze will run all packing methods on `cellpack/test-recipes/NM_Analysis_FigureB1.0.json -Examples: -* `analyze -o [PATH/TO/OUTPUT/FOLDER]` will create subfolders for each packing method at your output folder -* To run just one packing method: `analyze -o [PATH/TO/OUTPUT/FOLDER] -p jitter` -* To change the dimension of the packing: `analyze -r cellpack/test-recipes/NM_Analysis_FigureC1.json -o /Users/meganriel-mehan/Dropbox/cellPack/NM_Analysis_C_1 -d 3` -* Turn off plotly plot: `analyze -o [PATH/TO/OUTPUT/FOLDER] -ng` or `analyze -o [PATH/TO/OUTPUT/FOLDER] --no-grid-plot` +### Run pack code +1. example pack recipe : `pack -r cellpack/test-recipes/NM_Analysis_FigureB1.0.json -c packing-configs/run.json` ### Run conversion code * To convert to simularium and view at https://staging.simularium.allencell.org/viewer From 2d0e50596e38c7556488b57b4eb202cb95851606 Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Wed, 31 Aug 2022 14:08:14 -0700 Subject: [PATCH 2/7] update simulariumio version --- cellpack/autopack/upy/simularium/simularium_helper.py | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cellpack/autopack/upy/simularium/simularium_helper.py b/cellpack/autopack/upy/simularium/simularium_helper.py index 034bc344f..92462f317 100644 --- a/cellpack/autopack/upy/simularium/simularium_helper.py +++ b/cellpack/autopack/upy/simularium/simularium_helper.py @@ -1302,7 +1302,7 @@ def writeToFile(self, polygon, file_name, bb): time_units=UnitData("ns"), # nanoseconds spatial_units=UnitData("nm"), # nanometers ) - TrajectoryConverter(converted_data).write_JSON(file_name) + TrajectoryConverter(converted_data).save(file_name) def raycast(self, **kw): intersect = False diff --git a/setup.py b/setup.py index 922813d27..c782a32df 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ "panda3d==1.10.10", "pmw==2.0.1", "scipy>=1.6.2", - "simulariumio>=1.2.0", + "simulariumio>=1.6.2", "plotly>=5.3.1", "pycollada==0.7.2", "pyembree>=0.1.12", From 22690b1da85f528c50fd7506ac75c261bb191632 Mon Sep 17 00:00:00 2001 From: meganrm Date: Wed, 31 Aug 2022 18:20:38 -0700 Subject: [PATCH 3/7] change version to linux version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 922813d27..da97808b7 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ "simulariumio>=1.2.0", "plotly>=5.3.1", "pycollada==0.7.2", - "pyembree>=0.1.12", + "pyembree>=0.1.6", "pymunk>=6.2.0", "trimesh>=3.9.34", ] From a8bba1b6296710598964a9170caa80e32e556792 Mon Sep 17 00:00:00 2001 From: meganrm Date: Wed, 31 Aug 2022 18:29:36 -0700 Subject: [PATCH 4/7] =?UTF-8?q?Bump=20version:=201.0.1=20=E2=86=92=201.0.2?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- cellpack/__init__.py | 2 +- setup.cfg | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cellpack/__init__.py b/cellpack/__init__.py index f792e95fd..c819f5f9b 100644 --- a/cellpack/__init__.py +++ b/cellpack/__init__.py @@ -6,7 +6,7 @@ __email__ = "meganr@alleninstitute.org" # Do not edit this string manually, always use bumpversion # Details in CONTRIBUTING.md -__version__ = "1.0.1" +__version__ = "1.0.2" from .autopack.loaders.recipe_loader import RecipeLoader # noqa: F401 diff --git a/setup.cfg b/setup.cfg index f0ee3df4a..3e3549ccd 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.0.1 +current_version = 1.0.2 commit = True tag = True diff --git a/setup.py b/setup.py index da97808b7..44f73a632 100644 --- a/setup.py +++ b/setup.py @@ -98,6 +98,6 @@ url="https://github.com/mesoscope/cellpack", # Do not edit this string manually, always use bumpversion # Details in CONTRIBUTING.rst - version="1.0.1", + version="1.0.2", zip_safe=False, ) From 6935adf508144087e7724a9d3a6673b78a9a80ea Mon Sep 17 00:00:00 2001 From: meganrm Date: Wed, 31 Aug 2022 18:41:55 -0700 Subject: [PATCH 5/7] change pyembree version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 44f73a632..ffe041de6 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ "simulariumio>=1.2.0", "plotly>=5.3.1", "pycollada==0.7.2", - "pyembree>=0.1.6", + "pyembree>=0.1.8", "pymunk>=6.2.0", "trimesh>=3.9.34", ] From 81edc2bb77a39da17adeeb1fd7e76565b51fcf8e Mon Sep 17 00:00:00 2001 From: meganrm Date: Wed, 31 Aug 2022 18:42:12 -0700 Subject: [PATCH 6/7] =?UTF-8?q?Bump=20version:=201.0.2=20=E2=86=92=201.0.3?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- cellpack/__init__.py | 2 +- setup.cfg | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cellpack/__init__.py b/cellpack/__init__.py index c819f5f9b..65c4ef6c0 100644 --- a/cellpack/__init__.py +++ b/cellpack/__init__.py @@ -6,7 +6,7 @@ __email__ = "meganr@alleninstitute.org" # Do not edit this string manually, always use bumpversion # Details in CONTRIBUTING.md -__version__ = "1.0.2" +__version__ = "1.0.3" from .autopack.loaders.recipe_loader import RecipeLoader # noqa: F401 diff --git a/setup.cfg b/setup.cfg index 3e3549ccd..8ab46efbe 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.0.2 +current_version = 1.0.3 commit = True tag = True diff --git a/setup.py b/setup.py index ffe041de6..efa85a1af 100644 --- a/setup.py +++ b/setup.py @@ -98,6 +98,6 @@ url="https://github.com/mesoscope/cellpack", # Do not edit this string manually, always use bumpversion # Details in CONTRIBUTING.rst - version="1.0.2", + version="1.0.3", zip_safe=False, ) From 784086df843810da9d7e17a638a5f7bdaf887d51 Mon Sep 17 00:00:00 2001 From: Ruge Li <91452427+rugeli@users.noreply.github.com> Date: Fri, 2 Sep 2022 10:43:53 -0700 Subject: [PATCH 7/7] Update python version README.md Co-authored-by: Megan Riel-Mehan --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4df4f2e47..6acf02ca3 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ algorithm to pack molecular recipes 1. Install Conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html ### Setup -1. create a virtual env: `conda create -n autopack` +1. create a virtual env: `conda create -n autopack python=3.9` 2. `conda activate autopack` 3. `pip install -e .[dev]`