From c623cfef11a81de14a8f10d061616260b4fa9d2e Mon Sep 17 00:00:00 2001 From: Eljas Date: Sat, 15 Jun 2024 16:48:01 +0200 Subject: [PATCH 01/15] restrict tableone<=0.8.0 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index f7f8700c..9cb2248a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,7 +61,7 @@ dependencies = [ "dowhy", "fhiry", "pyampute", - "tableone", + "tableone<=0.8.0", "imbalanced-learn", "fknni", "python-dateutil", From 2e2df1bdf61c2649149ee51f663ea7447794e397 Mon Sep 17 00:00:00 2001 From: Eljas Date: Sun, 16 Jun 2024 10:14:06 +0200 Subject: [PATCH 02/15] maintenance: loosen tableone restriction --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9cb2248a..260cb51b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,7 +61,7 @@ dependencies = [ "dowhy", "fhiry", "pyampute", - "tableone<=0.8.0", + "tableone!=0.9.0", "imbalanced-learn", "fknni", "python-dateutil", From 6830d1827ac95cffc903d7814f424ffeb2a6580c Mon Sep 17 00:00:00 2001 From: Eljas Date: Sun, 16 Jun 2024 10:35:51 +0200 Subject: [PATCH 03/15] figure out if 0.9.0 breaks readthedocs --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 260cb51b..2465a015 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,7 +61,7 @@ dependencies = [ "dowhy", "fhiry", "pyampute", - "tableone!=0.9.0", + "tableone==0.8.0", "imbalanced-learn", "fknni", "python-dateutil", From 1c6da1128a16b971a482b511cc20b34eb88955ae Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Thu, 11 Jul 2024 18:56:05 +0200 Subject: [PATCH 04/15] >=0.9.1 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0d6e5f2d..29aeeb1c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,7 +62,7 @@ dependencies = [ "dowhy", "fhiry", "pyampute", - "tableone==0.8.0", + "tableone>=0.9.1", "imbalanced-learn", "fknni", "python-dateutil", From 76beefa299283d25d752fb6aa9792ba2fe434199 Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Thu, 11 Jul 2024 19:15:18 +0200 Subject: [PATCH 05/15] loosen restriction tableone --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 29aeeb1c..8a65763c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,7 +62,7 @@ dependencies = [ "dowhy", "fhiry", "pyampute", - "tableone>=0.9.1", + "tableone", "imbalanced-learn", "fknni", "python-dateutil", From 627f94abeb28c91a7059bfd5e6b24882b359320e Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Thu, 11 Jul 2024 21:42:18 +0200 Subject: [PATCH 06/15] just glimpse effect of np<2.0.0 in ci --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 8a65763c..861006c3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,6 +67,7 @@ dependencies = [ "fknni", "python-dateutil", "filelock", + "numpy<2.0.0" ] [project.optional-dependencies] From d0f4114229a7265f3b805cb6d114ad4f593992a1 Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Thu, 11 Jul 2024 21:47:33 +0200 Subject: [PATCH 07/15] revert to loosen tableone --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 861006c3..33c0ebc2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,8 +66,7 @@ dependencies = [ "imbalanced-learn", "fknni", "python-dateutil", - "filelock", - "numpy<2.0.0" + "filelock" ] [project.optional-dependencies] From 2dca8a382fcae44b2523cb1e6852bb870af2554c Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Thu, 11 Jul 2024 21:53:25 +0200 Subject: [PATCH 08/15] try to use uv again --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 5135ef47..1b92d647 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -12,7 +12,7 @@ build: post_install: # VIRTUAL_ENV needs to be set manually for now. # See https://github.com/readthedocs/readthedocs.org/pull/11152/ - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH pip install .[docs] + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install .[docs] sphinx: configuration: docs/conf.py fail_on_warning: false From 902b443778e15a2f88b26eeb6d72869bd9b6e67c Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Thu, 11 Jul 2024 22:10:23 +0200 Subject: [PATCH 09/15] restrict tableone to check incompat w/ uv --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 33c0ebc2..b629f0e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,7 +62,7 @@ dependencies = [ "dowhy", "fhiry", "pyampute", - "tableone", + "tableone<=0.8.0", "imbalanced-learn", "fknni", "python-dateutil", From 84fc557e8c184408a26186e6e06525f1c32c41a6 Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Thu, 11 Jul 2024 22:18:36 +0200 Subject: [PATCH 10/15] check quotations pip install --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 1b92d647..ccad9e35 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -12,7 +12,7 @@ build: post_install: # VIRTUAL_ENV needs to be set manually for now. # See https://github.com/readthedocs/readthedocs.org/pull/11152/ - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install .[docs] + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install ".[docs]" sphinx: configuration: docs/conf.py fail_on_warning: false From 4e7f0180c03e2dc5d89ec8e06759d117a948ab2a Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Thu, 11 Jul 2024 22:27:04 +0200 Subject: [PATCH 11/15] install rust toolchain --- .readthedocs.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.readthedocs.yml b/.readthedocs.yml index ccad9e35..072df7cc 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -5,6 +5,9 @@ build: python: "3.11" jobs: pre_build: + - apt-get update && apt-get install -y curl + - curl https://sh.rustup.rs -sSf | sh -s -- -y + - source $HOME/.cargo/env - python -c "import ehrapy" - pip freeze post_create_environment: From 368894e8c8c2856493ccde6557d8270190aba28e Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Thu, 11 Jul 2024 22:34:53 +0200 Subject: [PATCH 12/15] get rustc and cargo in rtd build --- .readthedocs.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 072df7cc..81662a72 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -5,13 +5,11 @@ build: python: "3.11" jobs: pre_build: - - apt-get update && apt-get install -y curl - - curl https://sh.rustup.rs -sSf | sh -s -- -y - - source $HOME/.cargo/env - python -c "import ehrapy" - pip freeze post_create_environment: - pip install uv + - apt update && apt install -y rustc cargo post_install: # VIRTUAL_ENV needs to be set manually for now. # See https://github.com/readthedocs/readthedocs.org/pull/11152/ From 68b6b27b4523cc8361021d2dd7f9a1d8a84050ba Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Thu, 11 Jul 2024 22:38:07 +0200 Subject: [PATCH 13/15] back to vanilla --- .readthedocs.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 81662a72..ccad9e35 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -9,7 +9,6 @@ build: - pip freeze post_create_environment: - pip install uv - - apt update && apt install -y rustc cargo post_install: # VIRTUAL_ENV needs to be set manually for now. # See https://github.com/readthedocs/readthedocs.org/pull/11152/ From 69d869c3b68ecd92c217610b5ed32071027503fd Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Wed, 17 Jul 2024 17:40:28 +0200 Subject: [PATCH 14/15] no uv, free t1 --- .readthedocs.yml | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index ccad9e35..f3429d22 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -12,7 +12,7 @@ build: post_install: # VIRTUAL_ENV needs to be set manually for now. # See https://github.com/readthedocs/readthedocs.org/pull/11152/ - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install ".[docs]" + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH pip install ".[docs]" sphinx: configuration: docs/conf.py fail_on_warning: false diff --git a/pyproject.toml b/pyproject.toml index 53521780..517a940a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,7 +61,7 @@ dependencies = [ "dowhy", "fhiry", "pyampute", - "tableone<=0.8.0", + "tableone", "imbalanced-learn", "fknni", "python-dateutil", From 0f73852b2374fbace429aadea09afbb42cdcc27e Mon Sep 17 00:00:00 2001 From: Eljas Roellin Date: Wed, 17 Jul 2024 17:53:15 +0200 Subject: [PATCH 15/15] remove quotation marks --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index f3429d22..5135ef47 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -12,7 +12,7 @@ build: post_install: # VIRTUAL_ENV needs to be set manually for now. # See https://github.com/readthedocs/readthedocs.org/pull/11152/ - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH pip install ".[docs]" + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH pip install .[docs] sphinx: configuration: docs/conf.py fail_on_warning: false