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Feature/zarr #73

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merged 51 commits into from Feb 1, 2023
Merged

Feature/zarr #73

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46cd5da
add netcdf dependency on windows and make sure it builds locally
toloudis Nov 27, 2022
5699e15
trying to make something work...
toloudis Nov 27, 2022
c4c16f7
try tensorstore instead
toloudis Nov 29, 2022
5cc4a54
remove awssdk for now
toloudis Nov 29, 2022
b1a63aa
add nasm for tensorstore
toloudis Nov 29, 2022
8b6e693
explicit add lbzstd
toloudis Nov 29, 2022
7a91c42
tensorstore try to use system tiff
toloudis Nov 29, 2022
ec22efd
fix build? removed CMAKE_INCLUDE_CURRENT_DIR
toloudis Nov 29, 2022
2232656
start to test tensorstore
toloudis Nov 29, 2022
122c72d
zarr reading test
toloudis Nov 29, 2022
b7c0d72
more build fix attempts
toloudis Nov 30, 2022
d036d00
clean up
toloudis Nov 30, 2022
74ba193
try gcc10
toloudis Nov 30, 2022
b3632c5
add zstd windows
toloudis Nov 30, 2022
7c72b4e
start to read some more of the metadata and consider multiscales
toloudis Nov 30, 2022
2c6492a
try to load lowest res zarr
toloudis Nov 30, 2022
b5335d6
output all the level dims
toloudis Nov 30, 2022
0195626
Merge remote-tracking branch 'origin/main' into feature/netcdf
toloudis Nov 30, 2022
971919c
new data path
toloudis Dec 1, 2022
dc063cb
needed trailing slash
toloudis Dec 1, 2022
72f4c2b
add a task queue class
toloudis Dec 3, 2022
4fe0f38
fix error
toloudis Dec 10, 2022
2242ea6
start to add a dialog for loading from cloud
toloudis Dec 10, 2022
0cb365c
add a loading dialog with some fake data
toloudis Dec 12, 2022
954fbfa
add some ui elements
toloudis Dec 13, 2022
8dd5f3b
Merge branch 'feature/render-series' into feature/zarr
toloudis Dec 22, 2022
66b0e23
work toward acquiring dimension metadata from cloud and presenting it
toloudis Dec 23, 2022
8c39d1e
add some logic around memory estimate and selecting levels
toloudis Dec 26, 2022
8e39a42
Merge branch 'main' into feature/zarr
toloudis Dec 26, 2022
9e3ecaa
add multiscale dims to all readers
toloudis Dec 28, 2022
0a76818
pass url down finally
toloudis Dec 29, 2022
c311a23
start a new load function interface to accommodate subregions
toloudis Dec 29, 2022
74f27af
hooking everything together bit by bit, code is still a bit spaghetti
toloudis Dec 30, 2022
0699202
DRY refactor
toloudis Dec 30, 2022
a8e7955
all loading goes through LoadSpec now
toloudis Jan 2, 2023
20d00e2
trying to make sure subregions work with zarr
toloudis Jan 2, 2023
258b0ad
remove hardcoded test files!
toloudis Jan 2, 2023
f1e05fc
refactor to move some implementation away from the gui code
toloudis Jan 2, 2023
c715b7c
use libczi as dll; could revert this change if zstd link issue is res…
toloudis Jan 6, 2023
87331fc
allow timeline widget to work with zarr in cloud
toloudis Jan 6, 2023
4ae5b85
Merge branch 'feature/zarr' of https://github.com/allen-cell-animated…
toloudis Jan 6, 2023
64aa4d6
Merge branch 'feature/render-series' into feature/zarr
toloudis Jan 8, 2023
ed5dcfe
prefer LoadSpec over string filepaths
toloudis Jan 9, 2023
659b007
post-merge fixup
toloudis Jan 9, 2023
f5b5f1b
Merge branch 'feature/render-series' into feature/zarr
toloudis Jan 9, 2023
6d9600d
remove redundant code
toloudis Jan 13, 2023
42ca4e0
remove unused data
toloudis Jan 13, 2023
33572f2
add deps for production build
toloudis Jan 13, 2023
f41289f
forgot gcc version
toloudis Jan 13, 2023
0bf8b8b
correct mistaken use of find_first_of and find_last_of
toloudis Jan 20, 2023
aa5dfe8
code review updates, all either comments or dead no-op code
toloudis Feb 1, 2023
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20 changes: 11 additions & 9 deletions .github/workflows/build_and_test.yml
View file
Open in desktop
Expand Up @@ -7,7 +7,7 @@ jobs:
docs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
submodules: "recursive"
- uses: ammaraskar/sphinx-action@master
Expand All @@ -33,7 +33,7 @@ jobs:
docs_pythonclient:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
submodules: "recursive"
- uses: ammaraskar/sphinx-action@master
Expand Down Expand Up @@ -66,7 +66,7 @@ jobs:
runs-on: ${{ matrix.os }}

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
submodules: "recursive"
- name: Install Qt
Expand All @@ -80,7 +80,7 @@ jobs:
CXX: clang++
run: |
export MACOSX_DEPLOYMENT_TARGET=10.15
brew install spdlog glm libtiff
brew install spdlog glm libtiff nasm
- name: macos build and test
if: matrix.os == 'macos-latest'
env:
Expand All @@ -107,12 +107,12 @@ jobs:
CC: gcc
CXX: g++
run: |
sudo apt-get install libspdlog-dev libglm-dev libgl1-mesa-dev libegl1-mesa-dev libtiff-dev
sudo apt-get install libspdlog-dev libglm-dev libgl1-mesa-dev libegl1-mesa-dev libtiff-dev libzstd-dev nasm
- name: linux build and test
if: matrix.os == 'ubuntu-latest'
env:
CC: gcc
CXX: g++
CC: gcc-10
CXX: g++-10
run: |
mkdir ./build
cd build
Expand All @@ -125,7 +125,9 @@ jobs:
env:
vc_arch: "x64"
run: |
vcpkg install --triplet x64-windows tiff glm zlib libjpeg-turbo liblzma spdlog
vcpkg install --triplet x64-windows tiff glm zlib libjpeg-turbo liblzma spdlog zstd
- name: windows get nasm
uses: ilammy/setup-nasm@v1
- name: windows build and test
if: matrix.os == 'windows-2019'
env:
Expand All @@ -149,7 +151,7 @@ jobs:
lint-and-test-pyclient:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v1
with:
Expand Down
20 changes: 11 additions & 9 deletions .github/workflows/tagged_master_release.yml
View file
Open in desktop
Expand Up @@ -13,7 +13,7 @@ jobs:
runs-on: ${{ matrix.os }}

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
submodules: "recursive"
- name: Install Qt
Expand All @@ -27,7 +27,7 @@ jobs:
CXX: clang++
run: |
export MACOSX_DEPLOYMENT_TARGET=10.15
brew install spdlog glm libtiff
brew install spdlog glm libtiff nasm
- name: macos build and test
if: matrix.os == 'macos-latest'
env:
Expand All @@ -54,12 +54,12 @@ jobs:
CC: gcc
CXX: g++
run: |
sudo apt-get install libspdlog-dev libglm-dev libgl1-mesa-dev libegl1-mesa-dev libtiff-dev
sudo apt-get install libspdlog-dev libglm-dev libgl1-mesa-dev libegl1-mesa-dev libtiff-dev libzstd-dev nasm
- name: linux build and test
if: matrix.os == 'ubuntu-latest'
env:
CC: gcc
CXX: g++
CC: gcc-10
CXX: g++-10
run: |
pwd
mkdir ./build
Expand All @@ -73,7 +73,9 @@ jobs:
env:
vc_arch: "x64"
run: |
vcpkg install --triplet x64-windows tiff glm zlib libjpeg-turbo liblzma spdlog
vcpkg install --triplet x64-windows tiff glm zlib libjpeg-turbo liblzma spdlog zstd
- name: windows get nasm
uses: ilammy/setup-nasm@v1
- name: windows build and test
if: matrix.os == 'windows-2019'
env:
Expand All @@ -97,7 +99,7 @@ jobs:
publish_pythonclient:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
submodules: "recursive"
- name: Install Python 3.9 version
Expand All @@ -123,7 +125,7 @@ jobs:
docs_pythonclient:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
submodules: "recursive"
- run: |
Expand Down Expand Up @@ -157,7 +159,7 @@ jobs:
docs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
submodules: "recursive"
- uses: ammaraskar/sphinx-action@master
Expand Down