From 2d0df1b936a9e7b83ecaa19748dc34df4e83d2b6 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Sun, 8 Sep 2024 09:50:39 -0400 Subject: [PATCH 01/14] try ydata-profiling --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index c3553dcb..031086af 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ def calculate_version(): ], extras_require={ 'dev': ['nose', 'numpy', 'scipy', 'tabulate', 'parameterized', - 'matplotlib', 'seaborn', 'pandas-profiling'], + 'matplotlib', 'seaborn', 'ydata-profiling'], }, classifiers=[ 'Intended Audience :: Developers', From 279be36f4f4afb5c729d91b970b9546c3afd7071 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Sun, 8 Sep 2024 09:54:17 -0400 Subject: [PATCH 02/14] ydata profiling --- pmlb/profiling.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pmlb/profiling.py b/pmlb/profiling.py index 9d80a7c1..6e9834dc 100644 --- a/pmlb/profiling.py +++ b/pmlb/profiling.py @@ -3,7 +3,7 @@ import subprocess import pandas as pd -from pandas_profiling import ProfileReport +from ydata_profiling import ProfileReport # Updated import from .pmlb import ( fetch_data, get_updated_datasets, last_commit_message From 13851becb92c58a39002fd4b71938fe1f8b7a2af Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Tue, 10 Sep 2024 14:39:22 -0400 Subject: [PATCH 03/14] install libjpeg-dev --- .github/workflows/pythonapp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 84337428..3f179665 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -41,7 +41,7 @@ jobs: run: | pip install ".[dev]" sudo apt-get update - sudo apt-get install libssl-dev libcurl4-openssl-dev + sudo apt-get install libssl-dev libcurl4-openssl-dev libjpeg-dev - name: Test with nose run: | nosetests -s -v From 265f484339eeae2017363cb6b2f468bb8856e07d Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Mon, 17 Feb 2025 13:18:08 -0500 Subject: [PATCH 04/14] put back install gcc --- .github/workflows/pythonapp.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 3f179665..7da56125 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -41,7 +41,7 @@ jobs: run: | pip install ".[dev]" sudo apt-get update - sudo apt-get install libssl-dev libcurl4-openssl-dev libjpeg-dev + sudo apt-get install libssl-dev libcurl4-openssl-dev - name: Test with nose run: | nosetests -s -v @@ -64,6 +64,12 @@ jobs: reticulate::py_discover_config() shell: Rscript {0} + - name: Install gcc + run: | + conda install -c conda-forge libstdcxx-ng + sudo rm /usr/lib/x86_64-linux-gnu/libstdc++.so.6 + sudo ln -s /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /usr/lib/x86_64-linux-gnu/libstdc++.so.6 + - name: Build site run: | Rscript -e 'print(reticulate::py_discover_config())' From 276cc1841684918977044ba141caf6a4d09aa66f Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Mon, 17 Feb 2025 13:26:37 -0500 Subject: [PATCH 05/14] update actions and python versions --- .github/workflows/pythonapp.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 7da56125..ec05bebb 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -15,7 +15,7 @@ jobs: steps: - name: Checkout code - uses: actions/checkout@v2 + uses: actions/checkout@v4 with: fetch-depth: 0 # lfs: true @@ -33,10 +33,10 @@ jobs: - name: Git LFS Pull run: git lfs pull - - name: Set up Python 3.8 - uses: actions/setup-python@v1 + - name: Set up Python 3.13 + uses: actions/setup-python@v5 with: - python-version: 3.8 + python-version: 3.13 - name: Install dependencies run: | pip install ".[dev]" From bda3955b36c9677936a8047adb3ee7a4c865a8a2 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Mon, 17 Feb 2025 13:33:09 -0500 Subject: [PATCH 06/14] python 3.12 --- .github/workflows/pythonapp.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index ec05bebb..cbf369d6 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -33,10 +33,10 @@ jobs: - name: Git LFS Pull run: git lfs pull - - name: Set up Python 3.13 + - name: Set up Python 3.12 uses: actions/setup-python@v5 with: - python-version: 3.13 + python-version: 3.12 - name: Install dependencies run: | pip install ".[dev]" From 96d9563f4d432e419d4531037f273754599cc879 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Mon, 17 Feb 2025 13:37:29 -0500 Subject: [PATCH 07/14] python 3.11 --- .github/workflows/pythonapp.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index cbf369d6..9b756c1d 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -33,10 +33,10 @@ jobs: - name: Git LFS Pull run: git lfs pull - - name: Set up Python 3.12 + - name: Set up Python 3.11 uses: actions/setup-python@v5 with: - python-version: 3.12 + python-version: 3.11 - name: Install dependencies run: | pip install ".[dev]" From cbf7e3cede699bc845086e394d084d9a46ed2f6f Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Mon, 17 Feb 2025 13:41:00 -0500 Subject: [PATCH 08/14] python 3.9 --- .github/workflows/pythonapp.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 9b756c1d..fbc77f38 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -33,10 +33,10 @@ jobs: - name: Git LFS Pull run: git lfs pull - - name: Set up Python 3.11 + - name: Set up Python 3.9 uses: actions/setup-python@v5 with: - python-version: 3.11 + python-version: 3.9 - name: Install dependencies run: | pip install ".[dev]" From 29865c510a8ffae1131f0037ada7ca46b0750e66 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Mon, 17 Feb 2025 13:56:23 -0500 Subject: [PATCH 09/14] libpng-dev --- .github/workflows/pythonapp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index fbc77f38..ad7f2286 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -41,7 +41,7 @@ jobs: run: | pip install ".[dev]" sudo apt-get update - sudo apt-get install libssl-dev libcurl4-openssl-dev + sudo apt-get install libssl-dev libcurl4-openssl-dev libpng-dev - name: Test with nose run: | nosetests -s -v From 351314f2d3ed4262dbadcccbdddb54436f044fc1 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Mon, 17 Feb 2025 14:43:27 -0500 Subject: [PATCH 10/14] try Nikola's suggestion --- .github/workflows/pythonapp.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index ad7f2286..b5e11dbf 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -67,8 +67,8 @@ jobs: - name: Install gcc run: | conda install -c conda-forge libstdcxx-ng - sudo rm /usr/lib/x86_64-linux-gnu/libstdc++.so.6 - sudo ln -s /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /usr/lib/x86_64-linux-gnu/libstdc++.so.6 + sudo mv /root/anaconda3/envs/live/lib/libstdc++.so.6 /root/anaconda3/envs/live/lib/old_libstdc++.so.6 + sudo ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /root/anaconda3/envs/live/lib/libstdc++.so.6 - name: Build site run: | From fa5e619c4891714bd7ecc8514f5511e4e71ab075 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Mon, 17 Feb 2025 15:46:21 -0500 Subject: [PATCH 11/14] remove gcc --- .github/workflows/pythonapp.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index b5e11dbf..b605fa0e 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -64,12 +64,6 @@ jobs: reticulate::py_discover_config() shell: Rscript {0} - - name: Install gcc - run: | - conda install -c conda-forge libstdcxx-ng - sudo mv /root/anaconda3/envs/live/lib/libstdc++.so.6 /root/anaconda3/envs/live/lib/old_libstdc++.so.6 - sudo ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /root/anaconda3/envs/live/lib/libstdc++.so.6 - - name: Build site run: | Rscript -e 'print(reticulate::py_discover_config())' From 3a7c434e4efef8412ce9bdede424f989fac03155 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Wed, 19 Feb 2025 13:54:25 -0500 Subject: [PATCH 12/14] temporary change: install pmlbr from github --- .github/workflows/pythonapp.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index b605fa0e..1c7378d0 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -53,7 +53,10 @@ jobs: - uses: r-lib/actions/setup-r@v2 - uses: r-lib/actions/setup-pandoc@v2 - name: Install R packages - run: Rscript -e 'install.packages(c("rmarkdown", "plotly", "dplyr", "htmlwidgets", "htmltools", "jsonlite", "readr", "DT", "remotes", "pmlbr"))' + run: | + install.packages(c("rmarkdown", "plotly", "dplyr", "htmlwidgets", "htmltools", "jsonlite", "readr", "DT", "remotes")) + remotes::install_github("EpistasisLab/pmlbr") + shell: Rscript {0} - name: Set up reticulate run: | From 0aa432a8c01846eb2e226ac9f4cd7ceb9ef7d17a Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Wed, 19 Feb 2025 15:14:04 -0500 Subject: [PATCH 13/14] GH_PAT --- .github/workflows/pythonapp.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 1c7378d0..a2770b6f 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -55,8 +55,11 @@ jobs: - name: Install R packages run: | install.packages(c("rmarkdown", "plotly", "dplyr", "htmlwidgets", "htmltools", "jsonlite", "readr", "DT", "remotes")) + Sys.setenv(GITHUB_PAT = Sys.getenv("GH_PAT")) remotes::install_github("EpistasisLab/pmlbr") shell: Rscript {0} + env: + GH_PAT: ${{ secrets.GH_PAT }} - name: Set up reticulate run: | From b7d56d14939894fb605ed3556fd7e99548504b8f Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Wed, 19 Feb 2025 15:34:18 -0500 Subject: [PATCH 14/14] GITHUB_PAT --- .github/workflows/pythonapp.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index a2770b6f..a492bd3b 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -53,13 +53,13 @@ jobs: - uses: r-lib/actions/setup-r@v2 - uses: r-lib/actions/setup-pandoc@v2 - name: Install R packages + env: + GITHUB_PAT: ${{ secrets.GH_PAT }} + shell: Rscript {0} run: | install.packages(c("rmarkdown", "plotly", "dplyr", "htmlwidgets", "htmltools", "jsonlite", "readr", "DT", "remotes")) - Sys.setenv(GITHUB_PAT = Sys.getenv("GH_PAT")) remotes::install_github("EpistasisLab/pmlbr") - shell: Rscript {0} - env: - GH_PAT: ${{ secrets.GH_PAT }} + - name: Set up reticulate run: |