From 25fe48258ba895ecd2439217861561380134927c Mon Sep 17 00:00:00 2001 From: alsmith Date: Wed, 15 Nov 2023 12:33:18 +0000 Subject: [PATCH 1/9] chore: pyarrow minimum to 14.0.1 --- environment.yml | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 157c1fe2..fb8b6c30 100644 --- a/environment.yml +++ b/environment.yml @@ -24,7 +24,7 @@ dependencies: - pandera<=0.17.1 - pydantic<=2.4.2 - plotly>5.0.0,<=5.15.0 - - pyarrow>8.0.0,<12.0.0 + - pyarrow>=14.0.1,<15.0.0 - pybedtools<=0.9.0 - pyranges<=0.0.127 - pysam>0.19.1,<=0.22.0 diff --git a/requirements.txt b/requirements.txt index 14054e24..e3a94a3e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ pandera<=0.17.2 pandera<=0.17.2 panel<=1.3.0 plotly>5.0.0,<=5.18.0 -pyarrow>8.0.0,<15.0.0 +pyarrow>=14.0.1,<15.0.0 pybedtools<=0.9.0 pydantic<=2.3.0 pydantic<=2.3.0 From 54fe1f7f772de48be6dbc93df28c62a4a7817f01 Mon Sep 17 00:00:00 2001 From: alsmith Date: Wed, 15 Nov 2023 12:38:28 +0000 Subject: [PATCH 2/9] fix(build): pyarrow 14.0.0 min --- environment.yml | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index fb8b6c30..c72a8bcc 100644 --- a/environment.yml +++ b/environment.yml @@ -24,7 +24,7 @@ dependencies: - pandera<=0.17.1 - pydantic<=2.4.2 - plotly>5.0.0,<=5.15.0 - - pyarrow>=14.0.1,<15.0.0 + - pyarrow>=14.0.0,<15.0.0 - pybedtools<=0.9.0 - pyranges<=0.0.127 - pysam>0.19.1,<=0.22.0 diff --git a/requirements.txt b/requirements.txt index e3a94a3e..4e658118 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ pandera<=0.17.2 pandera<=0.17.2 panel<=1.3.0 plotly>5.0.0,<=5.18.0 -pyarrow>=14.0.1,<15.0.0 +pyarrow>=14.0.0,<15.0.0 pybedtools<=0.9.0 pydantic<=2.3.0 pydantic<=2.3.0 From cb667a9f2caa2b643780c0ed3bf1fc3fd46a3627 Mon Sep 17 00:00:00 2001 From: alsmith Date: Wed, 15 Nov 2023 12:44:20 +0000 Subject: [PATCH 3/9] fix(build): removed ucsc-fetchchromsizes --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index c72a8bcc..1b4dd2ac 100644 --- a/environment.yml +++ b/environment.yml @@ -41,5 +41,4 @@ dependencies: - trim-galore<=0.6.10 - ucsc-bedgraphtobigwig - ucsc-bedtobigbed - - ucsc-fetchchromsizes - ujson<=5.7.0 From 766257b4f3ed9b36e499fddf3cccf4c984006179 Mon Sep 17 00:00:00 2001 From: alsmith Date: Wed, 15 Nov 2023 12:50:46 +0000 Subject: [PATCH 4/9] fix(build): install latest pyarrow through pip --- environment.yml | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 1b4dd2ac..d142b2f5 100644 --- a/environment.yml +++ b/environment.yml @@ -24,7 +24,7 @@ dependencies: - pandera<=0.17.1 - pydantic<=2.4.2 - plotly>5.0.0,<=5.15.0 - - pyarrow>=14.0.0,<15.0.0 + - pyarrow>=11.0.0,<15.0.0 - pybedtools<=0.9.0 - pyranges<=0.0.127 - pysam>0.19.1,<=0.22.0 diff --git a/requirements.txt b/requirements.txt index 4e658118..7c84c3d7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ pandera<=0.17.2 pandera<=0.17.2 panel<=1.3.0 plotly>5.0.0,<=5.18.0 -pyarrow>=14.0.0,<15.0.0 +pyarrow==14.0.* pybedtools<=0.9.0 pydantic<=2.3.0 pydantic<=2.3.0 From 8422cb006f7b5cedcf8e9b63f14d1f0a2433aa07 Mon Sep 17 00:00:00 2001 From: alsmith Date: Wed, 15 Nov 2023 13:01:47 +0000 Subject: [PATCH 5/9] fix(build): bumped pydantic --- environment.yml | 2 +- requirements.txt | 4 +--- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index d142b2f5..d700a9d5 100644 --- a/environment.yml +++ b/environment.yml @@ -22,7 +22,7 @@ dependencies: - pip<=22.2.2 - panel<=1.3.0 - pandera<=0.17.1 - - pydantic<=2.4.2 + - pydantic<=2.14.3 - plotly>5.0.0,<=5.15.0 - pyarrow>=11.0.0,<15.0.0 - pybedtools<=0.9.0 diff --git a/requirements.txt b/requirements.txt index 7c84c3d7..f1218207 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,13 +11,11 @@ more-itertools numpy<=1.23 pandas<=2.1.2 pandera<=0.17.2 -pandera<=0.17.2 panel<=1.3.0 plotly>5.0.0,<=5.18.0 pyarrow==14.0.* pybedtools<=0.9.0 -pydantic<=2.3.0 -pydantic<=2.3.0 +pydantic<=2.14.3 pyranges<=0.0.127 pysam>0.15.0,<=0.21.0 quarto From 573ce901ce9ebc86ba230a4a18aea28c7c2e0766 Mon Sep 17 00:00:00 2001 From: alsmith Date: Wed, 15 Nov 2023 13:02:59 +0000 Subject: [PATCH 6/9] fix(deps): wrong pydantic max version --- environment.yml | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index d700a9d5..2191148a 100644 --- a/environment.yml +++ b/environment.yml @@ -22,7 +22,7 @@ dependencies: - pip<=22.2.2 - panel<=1.3.0 - pandera<=0.17.1 - - pydantic<=2.14.3 + - pydantic<=2.5.0 - plotly>5.0.0,<=5.15.0 - pyarrow>=11.0.0,<15.0.0 - pybedtools<=0.9.0 diff --git a/requirements.txt b/requirements.txt index f1218207..f8840986 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ panel<=1.3.0 plotly>5.0.0,<=5.18.0 pyarrow==14.0.* pybedtools<=0.9.0 -pydantic<=2.14.3 +pydantic<=2.5.0 pyranges<=0.0.127 pysam>0.15.0,<=0.21.0 quarto From 87594de7e363b856e4a3a1b222b70ba51532d240 Mon Sep 17 00:00:00 2001 From: alsmith Date: Wed, 15 Nov 2023 13:12:38 +0000 Subject: [PATCH 7/9] fix(build): pinned pydantic --- environment.yml | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 2191148a..b0bd9c55 100644 --- a/environment.yml +++ b/environment.yml @@ -22,7 +22,7 @@ dependencies: - pip<=22.2.2 - panel<=1.3.0 - pandera<=0.17.1 - - pydantic<=2.5.0 + - pydantic==2.5.0 - plotly>5.0.0,<=5.15.0 - pyarrow>=11.0.0,<15.0.0 - pybedtools<=0.9.0 diff --git a/requirements.txt b/requirements.txt index f8840986..7cadcc47 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ panel<=1.3.0 plotly>5.0.0,<=5.18.0 pyarrow==14.0.* pybedtools<=0.9.0 -pydantic<=2.5.0 +pydantic==2.5.0 pyranges<=0.0.127 pysam>0.15.0,<=0.21.0 quarto From 1433f8f04192814755aa8f953d83c2f689d13ce0 Mon Sep 17 00:00:00 2001 From: asmith Date: Thu, 16 Nov 2023 13:07:47 +0000 Subject: [PATCH 8/9] chore(build): added log collection as artifact --- .github/workflows/CI.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index c56c8eae..c1952bb0 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -87,6 +87,13 @@ jobs: run: | pip install pytest-cov pytest-lazy-fixture pytest-order pytest-xdist pytest -vv -s --log-cli-level info --cov=./ --cov-report=xml --cores 2 + + - name: Archive production artifacts + uses: actions/upload-artifact@v3 + with: + name: capcruncher_output_logs + path: | + capcruncher_output/logs/* - name: Upload Coverage to Codecov uses: codecov/codecov-action@v3 From d984e38be2375e1ca853bf63727e3bb253a337cc Mon Sep 17 00:00:00 2001 From: asmith Date: Thu, 16 Nov 2023 13:57:48 +0000 Subject: [PATCH 9/9] chore(deps): pinned ibis, pydantic,ray --- environment.yml | 2 +- requirements.txt | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/environment.yml b/environment.yml index b0bd9c55..18ae2240 100644 --- a/environment.yml +++ b/environment.yml @@ -11,7 +11,7 @@ dependencies: - cookiecutter<=2.1.1 - fastqc<=0.12.1 - flash<=1.2.11 - - ibis-framework>=6.0.0,<=7.0.0 + - ibis-framework>6.1.0,<=7.0.0 - iced<=0.5.10 - joblib<=1.2.0 - loguru diff --git a/requirements.txt b/requirements.txt index 7cadcc47..d3323ba1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,7 @@ cooler<=0.9.2 duckdb<=0.9.1 grpcio >= 1.54.2 h5py -ibis-framework[duckdb] +ibis-framework[duckdb]>6.1.0,<=7.0.0 loguru<=0.7.2 more-itertools numpy<=1.23 @@ -13,13 +13,13 @@ pandas<=2.1.2 pandera<=0.17.2 panel<=1.3.0 plotly>5.0.0,<=5.18.0 -pyarrow==14.0.* +pyarrow>11.0.0,<14.0.0 pybedtools<=0.9.0 -pydantic==2.5.0 +pydantic>2.4.0,<2.5.0 pyranges<=0.0.127 pysam>0.15.0,<=0.21.0 quarto -ray<=2.8.0 +ray>=2.8.0 seaborn<=0.12.2 snakemake<=7.32.4 tqdm<=4.65.0