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[IA-4586] Try to fix the install of pytz #462

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merged 4 commits into from
Oct 6, 2023
Merged

[IA-4586] Try to fix the install of pytz #462

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c3cfc23
try to fix the install of pytz
LizBaldo Oct 5, 2023
e0bc275
do not force reinstall
LizBaldo Oct 5, 2023
47714b4
pin pytz to previous version
LizBaldo Oct 6, 2023
8a400cd
add changelogs
LizBaldo Oct 6, 2023
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8 changes: 4 additions & 4 deletions config/conf.json
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Expand Up @@ -47,7 +47,7 @@
"hail"
]
},
"version" : "1.1.3",
"version" : "1.1.4",
"automated_flags" : {
"generate_docs" : true,
"include_in_ui" : true,
Expand All @@ -68,7 +68,7 @@
"scikit-learn"
]
},
"version" : "1.1.3",
"version" : "1.1.4",
"automated_flags" : {
"generate_docs" : true,
"include_in_ui" : true,
Expand Down Expand Up @@ -124,7 +124,7 @@
"packages" : {

},
"version" : "2.3.3",
"version" : "2.3.4",
"automated_flags" : {
"include_in_ui" : true,
"generate_docs" : true,
Expand All @@ -143,7 +143,7 @@
"packages" : {

},
"version" : "2.2.3",
"version" : "2.2.4",
"automated_flags" : {
"include_in_ui" : false,
"generate_docs" : false,
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7 changes: 7 additions & 0 deletions terra-jupyter-aou/CHANGELOG.md
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@@ -1,3 +1,10 @@
## 2.2.4 - 2023-10-06
- Update `terra-jupyter-gatk` to `2.3.4`
- Update `terra-jupyter-python` to `1.1.4`
- Downgrade pytz to `2023.3`

Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.4`

## 2.2.3 - 2023-10-03
- Update `terra-jupyter-gatk` to `2.3.3`
- Update `terra-jupyter-python` to `1.1.3`
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2 changes: 1 addition & 1 deletion terra-jupyter-aou/Dockerfile
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@@ -1,4 +1,4 @@
FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.3
FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.4

USER root

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6 changes: 6 additions & 0 deletions terra-jupyter-gatk/CHANGELOG.md
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@@ -1,3 +1,9 @@
## 2.3.4 - 2023-10-06
- Update `terra-jupyter-python` to `1.1.4`
- Downgrade pytz to `2023.3`

Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.4`

## 2.3.3 - 2023-10-03
- Update `terra-jupyter-r` to `2.2.3`
- Update `terra-jupyter-python` to `1.1.3`
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6 changes: 3 additions & 3 deletions terra-jupyter-gatk/Dockerfile
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@@ -1,4 +1,4 @@
FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.3 AS python
FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.4 AS python

FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.3

Expand Down Expand Up @@ -82,11 +82,11 @@ RUN patch -u /opt/conda/lib/python3.10/site-packages/vqsr_cnn/vqsr_cnn/models.py
# Older version of nbconvert fail to convert notebooks to html
RUN pip3 install "nbconvert>=7.7.3"


ENV PIP_USER=true

ENV USER jupyter

USER $USER

# pytz seems to have a metadata error when installing. Force-reinstalling fixes this.
RUN pip3 install --force-reinstall pytz

6 changes: 6 additions & 0 deletions terra-jupyter-hail/CHANGELOG.md
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@@ -1,3 +1,9 @@
## 1.1.4 - 2023-10-06
- Update `terra-jupyter-python` to `1.1.4`
- Downgrade pytz to `2023.3`

Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.1.4`

## 1.1.3 - 2023-10-03
- Update `terra-jupyter-python` to `1.1.3`
- Update `terra-jupyter-base` to `1.1.3`
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2 changes: 1 addition & 1 deletion terra-jupyter-hail/Dockerfile
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@@ -1,4 +1,4 @@
FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.3
FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.4

USER root

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6 changes: 6 additions & 0 deletions terra-jupyter-python/CHANGELOG.md
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@@ -1,3 +1,9 @@
## 1.1.4 - 2023-10-06
- Downgrade pytz to `2023.3`

Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.4`


## 1.1.3 - 2023-10-03
- Update `terra-jupyter-base` to `1.1.3`
- Downgrade notebook to `6.5.4` and jupyterlab-server to `2.23.0`
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3 changes: 1 addition & 2 deletions terra-jupyter-python/Dockerfile
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Expand Up @@ -49,8 +49,7 @@ ENV PIP_USER=true
# Enable Intel oneDNN optimizatoin by default
ENV TF_ENABLE_ONEDNN_OPTS=1

# pytz seems to have a metadata error when installing. Force-reinstalling fixes this.
RUN pip3 install --force-reinstall pytz


# Note: this entrypoint is provided for running Jupyter independently of Leonardo.
# When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable
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2 changes: 1 addition & 1 deletion terra-jupyter-python/requirements.txt
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Expand Up @@ -27,7 +27,7 @@ Cython
pysam
--no-binary=pysam
python-dateutil
pytz
pytz==2023.3
pyvcf3
theano
tqdm
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