From 280adf6e7260c69acd93f8fc4414cbbd569860a4 Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Tue, 5 Sep 2023 14:59:13 -0400 Subject: [PATCH 01/12] update si_env for mac and windows, add error log --- installation_tips/check_your_install.py | 4 ++-- .../full_spikeinterface_environment_mac.yml | 13 +++++-------- .../full_spikeinterface_environment_windows.yml | 12 +++++------- 3 files changed, 12 insertions(+), 17 deletions(-) diff --git a/installation_tips/check_your_install.py b/installation_tips/check_your_install.py index 20809ec6c0..c4aa860979 100644 --- a/installation_tips/check_your_install.py +++ b/installation_tips/check_your_install.py @@ -103,8 +103,8 @@ def _clean(): try: func() done = '...OK' - except: - done = '...Fail' + except Exception as err: + done = f'...Fail, Error: {err}' print(label, done) if platform.system() == "Windows": diff --git a/installation_tips/full_spikeinterface_environment_mac.yml b/installation_tips/full_spikeinterface_environment_mac.yml index 8b872981aa..867de7f98b 100755 --- a/installation_tips/full_spikeinterface_environment_mac.yml +++ b/installation_tips/full_spikeinterface_environment_mac.yml @@ -3,12 +3,10 @@ channels: - conda-forge - defaults dependencies: - - python=3.9 + - python=3.10 - pip>=21.0 - # numpy 1.21 break numba which break tridesclous - - numpy<1.22 - # joblib 1.2 is breaking hdbscan - - joblib=1.1 + - numpy + - joblib - tqdm - matplotlib - h5py @@ -30,13 +28,12 @@ dependencies: - pip: # - PyQt5 - ephyviewer - - neo>=0.11 - - elephant>=0.10.0 + - neo>=0.12 - probeinterface>=0.2.11 - MEArec>=1.8 - spikeinterface[full, widgets] - spikeinterface-gui - - tridesclous>=1.6.6.1 + - tridesclous>=1.6.8 # - phy==2.0b5 - mountainsort4>=1.0.0 - mountainsort5>=0.3.0 diff --git a/installation_tips/full_spikeinterface_environment_windows.yml b/installation_tips/full_spikeinterface_environment_windows.yml index 8c793edcb1..38c26e6a78 100755 --- a/installation_tips/full_spikeinterface_environment_windows.yml +++ b/installation_tips/full_spikeinterface_environment_windows.yml @@ -3,12 +3,11 @@ channels: - conda-forge - defaults dependencies: - - python=3.9 + - python=3.10 - pip>=21.0 # numpy 1.21 break numba which break tridesclous - - numpy<1.22 - # joblib 1.2 is breaking hdbscan - - joblib=1.1 + - numpy + - joblib - tqdm - matplotlib - h5py @@ -26,11 +25,10 @@ dependencies: - ipympl - pip: - ephyviewer - - neo>=0.11 - - elephant>=0.10.0 + - neo>=0.12 - probeinterface>=0.2.11 - MEArec>=1.8 - spikeinterface[full, widgets] - spikeinterface-gui - - tridesclous>=1.6.6.1 + - tridesclous>=1.6.8 # - phy==2.0b5 From 963914e4f25130e098aae650d8e38084191ed499 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 5 Sep 2023 19:07:18 +0000 Subject: [PATCH 02/12] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- installation_tips/check_your_install.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/installation_tips/check_your_install.py b/installation_tips/check_your_install.py index c4aa860979..2b13a941cd 100644 --- a/installation_tips/check_your_install.py +++ b/installation_tips/check_your_install.py @@ -104,7 +104,7 @@ def _clean(): func() done = '...OK' except Exception as err: - done = f'...Fail, Error: {err}' + done = f'...Fail, Error: {err}' print(label, done) if platform.system() == "Windows": From 842de8db06b6268651e382af81e1dfb3cfb06822 Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Wed, 6 Sep 2023 07:31:11 -0400 Subject: [PATCH 03/12] comment out mountainsort4/5 fail on pip install for mac --- installation_tips/full_spikeinterface_environment_mac.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/installation_tips/full_spikeinterface_environment_mac.yml b/installation_tips/full_spikeinterface_environment_mac.yml index 867de7f98b..7ce4a149cc 100755 --- a/installation_tips/full_spikeinterface_environment_mac.yml +++ b/installation_tips/full_spikeinterface_environment_mac.yml @@ -35,5 +35,5 @@ dependencies: - spikeinterface-gui - tridesclous>=1.6.8 # - phy==2.0b5 - - mountainsort4>=1.0.0 - - mountainsort5>=0.3.0 + # - mountainsort4>=1.0.0 isosplit5 fails on pip install for mac + # - mountainsort5>=0.3.0 From 55e8c51d16dfc2be6ca3dadc18d630fa9507fda1 Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Wed, 6 Sep 2023 21:14:20 -0400 Subject: [PATCH 04/12] update linux and draft a github action --- .github/workflows/installation-tips-test.yml | 43 +++++++++++++++++++ ...spikeinterface_environment_linux_dandi.yml | 11 ++--- 2 files changed, 47 insertions(+), 7 deletions(-) create mode 100644 .github/workflows/installation-tips-test.yml diff --git a/.github/workflows/installation-tips-test.yml b/.github/workflows/installation-tips-test.yml new file mode 100644 index 0000000000..efee9ef370 --- /dev/null +++ b/.github/workflows/installation-tips-test.yml @@ -0,0 +1,43 @@ +name: Creates Conda Install for Installation Tips + +on: + workflow_dispatch: + pull_request: + types: [synchronize, opened, reopened] + schedule: + - cron: "0 12 * * *" # Daily at noon UTC + +jobs: + testing: + name: Build Conda Env on ${{ matrix.os }} OS + runs-on: ${{ matrix.os }} + defaults: + run: + shell: bash -el {0} + strategy: + fail-fast: false + matrix: + include: + - os: ubuntu-latest + label: linux_dandi + - os: macos-latest + label: mac + - os: windows-latest + label: windows + steps: + - uses: actions/checkout@v3 + - name: Set up Python 3.10 + uses: actions/setup-python@v3 + with: + python-version: '3.10' + - name: Add conda to system path + run: | + # $CONDA is an environment variable pointing to the root of the miniconda directory + echo $CONDA/bin >> $GITHUB_PATH + + - name: Test Conda Environment Creation + uses: conda-incubator/setup-miniconda@v2.2.0 + with: + environment-file: ./installations_tips/full_spikeinterface_environment_${{ matrix.label }}.yml + + \ No newline at end of file diff --git a/installation_tips/full_spikeinterface_environment_linux_dandi.yml b/installation_tips/full_spikeinterface_environment_linux_dandi.yml index d402f6805f..2ed176b16c 100755 --- a/installation_tips/full_spikeinterface_environment_linux_dandi.yml +++ b/installation_tips/full_spikeinterface_environment_linux_dandi.yml @@ -3,13 +3,11 @@ channels: - conda-forge - defaults dependencies: - - python=3.9 + - python=3.10 - pip>=21.0 - mamba - # numpy 1.22 break numba which break tridesclous - numpy<1.22 - # joblib 1.2 is breaking hdbscan - - joblib=1.1 + - joblib - tqdm - matplotlib - h5py @@ -31,12 +29,11 @@ dependencies: - ipympl - pip: - ephyviewer - - neo>=0.11 - - elephant>=0.10.0 + - neo>=0.12 - probeinterface>=0.2.11 - MEArec>=1.8 - spikeinterface[full, widgets] - spikeinterface-gui - - tridesclous>=1.6.6.1 + - tridesclous>=1.6.8 - spyking-circus>=1.1.0 # - phy==2.0b5 From 807f0ad3e4e93c524eac28e376e2253b72e6aa0f Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Wed, 6 Sep 2023 21:22:48 -0400 Subject: [PATCH 05/12] test on push for github actions --- installation-tips-test.yml | 40 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 installation-tips-test.yml diff --git a/installation-tips-test.yml b/installation-tips-test.yml new file mode 100644 index 0000000000..2628b08529 --- /dev/null +++ b/installation-tips-test.yml @@ -0,0 +1,40 @@ +name: Creates Conda Install for Installation Tips + +on: + workflow_dispatch: + push: + schedule: + - cron: "0 12 * * *" # Daily at noon UTC + +jobs: + testing: + name: Build Conda Env on ${{ matrix.os }} OS + runs-on: ${{ matrix.os }} + defaults: + run: + shell: bash -el {0} + strategy: + fail-fast: false + matrix: + include: + - os: ubuntu-latest + label: linux_dandi + - os: macos-latest + label: mac + - os: windows-latest + label: windows + steps: + - uses: actions/checkout@v3 + - name: Set up Python 3.10 + uses: actions/setup-python@v3 + with: + python-version: '3.10' + - name: Add conda to system path + run: | + # $CONDA is an environment variable pointing to the root of the miniconda directory + echo $CONDA/bin >> $GITHUB_PATH + + - name: Test Conda Environment Creation + uses: conda-incubator/setup-miniconda@v2.2.0 + with: + environment-file: ./installations_tips/full_spikeinterface_environment_${{ matrix.label }}.yml From 6a37b0da0c9483171893bfe9c3e89ea51af35a44 Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Wed, 6 Sep 2023 21:29:36 -0400 Subject: [PATCH 06/12] fix misaligned run --- installation-tips-test.yml | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/installation-tips-test.yml b/installation-tips-test.yml index 2628b08529..c6c32b812b 100644 --- a/installation-tips-test.yml +++ b/installation-tips-test.yml @@ -7,7 +7,7 @@ on: - cron: "0 12 * * *" # Daily at noon UTC jobs: - testing: + installation-tips-testing: name: Build Conda Env on ${{ matrix.os }} OS runs-on: ${{ matrix.os }} defaults: @@ -25,15 +25,9 @@ jobs: label: windows steps: - uses: actions/checkout@v3 - - name: Set up Python 3.10 - uses: actions/setup-python@v3 + uses: actions/setup-python@v4 with: python-version: '3.10' - - name: Add conda to system path - run: | - # $CONDA is an environment variable pointing to the root of the miniconda directory - echo $CONDA/bin >> $GITHUB_PATH - - name: Test Conda Environment Creation uses: conda-incubator/setup-miniconda@v2.2.0 with: From 918cd67c699eb7ce353a90d6d68408a4b0734e8b Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Wed, 6 Sep 2023 21:32:05 -0400 Subject: [PATCH 07/12] fix my folder mistake --- .github/workflows/installation-tips-test.yml | 15 ++------- installation-tips-test.yml | 34 -------------------- 2 files changed, 3 insertions(+), 46 deletions(-) delete mode 100644 installation-tips-test.yml diff --git a/.github/workflows/installation-tips-test.yml b/.github/workflows/installation-tips-test.yml index efee9ef370..c6c32b812b 100644 --- a/.github/workflows/installation-tips-test.yml +++ b/.github/workflows/installation-tips-test.yml @@ -2,13 +2,12 @@ name: Creates Conda Install for Installation Tips on: workflow_dispatch: - pull_request: - types: [synchronize, opened, reopened] + push: schedule: - cron: "0 12 * * *" # Daily at noon UTC jobs: - testing: + installation-tips-testing: name: Build Conda Env on ${{ matrix.os }} OS runs-on: ${{ matrix.os }} defaults: @@ -26,18 +25,10 @@ jobs: label: windows steps: - uses: actions/checkout@v3 - - name: Set up Python 3.10 - uses: actions/setup-python@v3 + uses: actions/setup-python@v4 with: python-version: '3.10' - - name: Add conda to system path - run: | - # $CONDA is an environment variable pointing to the root of the miniconda directory - echo $CONDA/bin >> $GITHUB_PATH - - name: Test Conda Environment Creation uses: conda-incubator/setup-miniconda@v2.2.0 with: environment-file: ./installations_tips/full_spikeinterface_environment_${{ matrix.label }}.yml - - \ No newline at end of file diff --git a/installation-tips-test.yml b/installation-tips-test.yml deleted file mode 100644 index c6c32b812b..0000000000 --- a/installation-tips-test.yml +++ /dev/null @@ -1,34 +0,0 @@ -name: Creates Conda Install for Installation Tips - -on: - workflow_dispatch: - push: - schedule: - - cron: "0 12 * * *" # Daily at noon UTC - -jobs: - installation-tips-testing: - name: Build Conda Env on ${{ matrix.os }} OS - runs-on: ${{ matrix.os }} - defaults: - run: - shell: bash -el {0} - strategy: - fail-fast: false - matrix: - include: - - os: ubuntu-latest - label: linux_dandi - - os: macos-latest - label: mac - - os: windows-latest - label: windows - steps: - - uses: actions/checkout@v3 - uses: actions/setup-python@v4 - with: - python-version: '3.10' - - name: Test Conda Environment Creation - uses: conda-incubator/setup-miniconda@v2.2.0 - with: - environment-file: ./installations_tips/full_spikeinterface_environment_${{ matrix.label }}.yml From b815ed91c0a8b2f52a44fb9f83b45eb2987184cf Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Wed, 6 Sep 2023 21:35:20 -0400 Subject: [PATCH 08/12] fix spacing of action --- .github/workflows/installation-tips-test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/installation-tips-test.yml b/.github/workflows/installation-tips-test.yml index c6c32b812b..7285dfa9f5 100644 --- a/.github/workflows/installation-tips-test.yml +++ b/.github/workflows/installation-tips-test.yml @@ -28,7 +28,7 @@ jobs: uses: actions/setup-python@v4 with: python-version: '3.10' - - name: Test Conda Environment Creation - uses: conda-incubator/setup-miniconda@v2.2.0 - with: + - name: Test Conda Environment Creation + uses: conda-incubator/setup-miniconda@v2.2.0 + with: environment-file: ./installations_tips/full_spikeinterface_environment_${{ matrix.label }}.yml From 2bbead38f3309428bceb4819c9328b64501915ae Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Wed, 6 Sep 2023 21:36:38 -0400 Subject: [PATCH 09/12] final fix I hope --- .github/workflows/installation-tips-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/installation-tips-test.yml b/.github/workflows/installation-tips-test.yml index 7285dfa9f5..c3c70db66e 100644 --- a/.github/workflows/installation-tips-test.yml +++ b/.github/workflows/installation-tips-test.yml @@ -25,7 +25,7 @@ jobs: label: windows steps: - uses: actions/checkout@v3 - uses: actions/setup-python@v4 + - uses: actions/setup-python@v4 with: python-version: '3.10' - name: Test Conda Environment Creation From 03f9da463901b9a33a6c27b50d93e80d569c0f4a Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Wed, 6 Sep 2023 21:40:10 -0400 Subject: [PATCH 10/12] delete on push, deleting trailing white --- .github/workflows/installation-tips-test.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/installation-tips-test.yml b/.github/workflows/installation-tips-test.yml index c3c70db66e..a985a6d60d 100644 --- a/.github/workflows/installation-tips-test.yml +++ b/.github/workflows/installation-tips-test.yml @@ -2,7 +2,6 @@ name: Creates Conda Install for Installation Tips on: workflow_dispatch: - push: schedule: - cron: "0 12 * * *" # Daily at noon UTC @@ -31,4 +30,4 @@ jobs: - name: Test Conda Environment Creation uses: conda-incubator/setup-miniconda@v2.2.0 with: - environment-file: ./installations_tips/full_spikeinterface_environment_${{ matrix.label }}.yml + environment-file: ./installations_tips/full_spikeinterface_environment_${{ matrix.label }}.yml \ No newline at end of file From cf7ee82752bdb32d6960676f0599651eee52b98b Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Thu, 7 Sep 2023 05:38:18 -0400 Subject: [PATCH 11/12] local pre-commit --- .github/workflows/installation-tips-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/installation-tips-test.yml b/.github/workflows/installation-tips-test.yml index a985a6d60d..64a4e45270 100644 --- a/.github/workflows/installation-tips-test.yml +++ b/.github/workflows/installation-tips-test.yml @@ -4,7 +4,7 @@ on: workflow_dispatch: schedule: - cron: "0 12 * * *" # Daily at noon UTC - + jobs: installation-tips-testing: name: Build Conda Env on ${{ matrix.os }} OS @@ -30,4 +30,4 @@ jobs: - name: Test Conda Environment Creation uses: conda-incubator/setup-miniconda@v2.2.0 with: - environment-file: ./installations_tips/full_spikeinterface_environment_${{ matrix.label }}.yml \ No newline at end of file + environment-file: ./installations_tips/full_spikeinterface_environment_${{ matrix.label }}.yml From badfadc523edece56f5fa0d21abb4ddd76b11998 Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Wed, 13 Sep 2023 16:59:26 +0200 Subject: [PATCH 12/12] Update .github/workflows/installation-tips-test.yml --- .github/workflows/installation-tips-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/installation-tips-test.yml b/.github/workflows/installation-tips-test.yml index 64a4e45270..0e522e6baa 100644 --- a/.github/workflows/installation-tips-test.yml +++ b/.github/workflows/installation-tips-test.yml @@ -3,7 +3,7 @@ name: Creates Conda Install for Installation Tips on: workflow_dispatch: schedule: - - cron: "0 12 * * *" # Daily at noon UTC + - cron: "0 12 * * 0" # Weekly at noon UTC on Sundays jobs: installation-tips-testing: