From 86746ee41f696cacd15aaaaa0a4081a0a097a971 Mon Sep 17 00:00:00 2001 From: juhuntenburg Date: Wed, 13 Oct 2021 11:02:59 +0200 Subject: [PATCH 1/4] Bump version --- iblvideo/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/iblvideo/__init__.py b/iblvideo/__init__.py index e228b25..d52797e 100644 --- a/iblvideo/__init__.py +++ b/iblvideo/__init__.py @@ -1,5 +1,5 @@ -__version__ = '2.0.0' # This is the only place where the version is hard coded, only adapt here +__version__ = '2.1.0' # This is the only place where the version is hard coded, only adapt here import deeplabcut From ca2ae6dc039dbe439e74a6499692a755055f5224 Mon Sep 17 00:00:00 2001 From: juhuntenburg Date: Wed, 13 Oct 2021 11:21:41 +0200 Subject: [PATCH 2/4] Remove Dlc Qc from this task --- iblvideo/run.py | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/iblvideo/run.py b/iblvideo/run.py index 085ca75..058873f 100644 --- a/iblvideo/run.py +++ b/iblvideo/run.py @@ -245,30 +245,6 @@ def run_session(session_id, machine=None, cams=('left', 'body', 'right'), one=No if remove_videos is True: shutil.rmtree(session_path.joinpath('raw_video_data'), ignore_errors=True) - # Run DLC QC - # Download camera times and then force qc to use local data as dlc might not have - # been updated on FlatIron at this stage - try: - datasets = one.type2datasets(session_id, 'camera.times') - one.load_datasets(session_id, datasets=datasets, download_only=True) - alf_path = one.eid2path(session_id).joinpath('alf') - for cam in cams: - # Only run if dlc actually exists - if alf_path.joinpath(f'_ibl_{cam}Camera.dlc.pqt').exists(): - qc = DlcQC(session_id, cam, one=one, download_data=False) - with warnings.catch_warnings(): - warnings.simplefilter("ignore", category=RuntimeWarning) - qc.run(update=True) - except AssertionError: - # If the camera.times don't exist we cannot run QC, but the DLC task shouldn't fail - # Make sure to not overwrite the task log if that has already been updated - tdict = one.alyx.rest('tasks', 'list', - django=f"name__icontains,DLC,session__id,{session_id}", - no_cache=True)[0] - patch_data = {'log': tdict['log'] + '\n\n' + traceback.format_exc()} - one.alyx.rest('tasks', 'partial_update', id=tdict['id'], data=patch_data, - no_cache=True) - except BaseException: # Make sure to not overwrite the task log if that has already been updated tdict = one.alyx.rest('tasks', 'list', From 2957c8e075145e2c01cc60701a980fdfb261a0cd Mon Sep 17 00:00:00 2001 From: juhuntenburg Date: Wed, 13 Oct 2021 11:21:49 +0200 Subject: [PATCH 3/4] Update Docker --- docker/Dockerfile.v2.0 | 2 +- docker/Dockerfile.v2.1 | 11 +++++++++++ docker/docker-compose.yaml | 6 +++--- 3 files changed, 15 insertions(+), 4 deletions(-) create mode 100644 docker/Dockerfile.v2.1 diff --git a/docker/Dockerfile.v2.0 b/docker/Dockerfile.v2.0 index 230252c..c2abf84 100644 --- a/docker/Dockerfile.v2.0 +++ b/docker/Dockerfile.v2.0 @@ -7,5 +7,5 @@ COPY me_test_data me_test_data COPY dlc_test_data_v2.0 dlc_test_data_v2.0 # clone the code -RUN git clone --depth 1 --single-branch --branch one2 https://github.com/int-brain-lab/iblvideo.git +RUN git clone --depth 1 --single-branch --branch v2.0.0 https://github.com/int-brain-lab/iblvideo.git ENV PYTHONPATH=/iblvideo diff --git a/docker/Dockerfile.v2.1 b/docker/Dockerfile.v2.1 new file mode 100644 index 0000000..8b836a6 --- /dev/null +++ b/docker/Dockerfile.v2.1 @@ -0,0 +1,11 @@ +#docker build -t internationalbrainlab/dlc:v2.1 -f Dockerfile.v2.1 --no-cache . +FROM internationalbrainlab/dlc:base + +# copy the weights and test data +COPY weights_v2.1 weights_v2.1 +COPY me_test_data me_test_data +COPY dlc_test_data_v2.1 dlc_test_data_v2.1 + +# clone the code +RUN git clone --depth 1 --single-branch --branch v2.1.0 https://github.com/int-brain-lab/iblvideo.git +ENV PYTHONPATH=/iblvideo diff --git a/docker/docker-compose.yaml b/docker/docker-compose.yaml index 87441d7..30ee255 100644 --- a/docker/docker-compose.yaml +++ b/docker/docker-compose.yaml @@ -17,14 +17,14 @@ services: - ~/Documents/PYTHON/iblvideo:/iblvideo - ~:/root queue: - image: internationalbrainlab/dlc:v2.0 - command: python3 -c "from iblvideo import run_queue; run_queue(target_versions=('1.2.0', '2.0.0'))" + image: internationalbrainlab/dlc:v2.1 + command: python3 -c "from iblvideo import run_queue; run_queue(target_versions=('1.2.0', '2.1.0'))" runtime: nvidia volumes: - ~:/root - /mnt/s0/Data/FlatIron:/mnt/s0/Data/FlatIron test: - image: internationalbrainlab/dlc:v2.0 + image: internationalbrainlab/dlc:v2.1 command: bash -c "nvcc --version; pytest -s /iblvideo/iblvideo/tests" runtime: nvidia volumes: From 5e89eecc1bdb51e6b322fd2148bdeee331adafb1 Mon Sep 17 00:00:00 2001 From: juhuntenburg Date: Wed, 13 Oct 2021 14:13:57 +0100 Subject: [PATCH 4/4] docker-compose --- docker/docker-compose.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/docker-compose.yaml b/docker/docker-compose.yaml index 30ee255..e058bb1 100644 --- a/docker/docker-compose.yaml +++ b/docker/docker-compose.yaml @@ -18,7 +18,7 @@ services: - ~:/root queue: image: internationalbrainlab/dlc:v2.1 - command: python3 -c "from iblvideo import run_queue; run_queue(target_versions=('1.2.0', '2.1.0'))" + command: python3 -c "from iblvideo import run_queue; run_queue(target_versions=('1.2.0', '2.0.0', '2.1.0'))" runtime: nvidia volumes: - ~:/root