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Add boto3 dependency, add venv/.venv to .gitignore #239

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merged 8 commits into from
Jul 11, 2024
Merged

Add boto3 dependency, add venv/.venv to .gitignore #239

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708cc41
Added missing boto3 dependency for gempyor, GH-238
TimothyWillard Jun 21, 2024
0b32f2e
Moved .Rproj.user gitignore to the right place, added venv & .venv fo…
TimothyWillard Jun 21, 2024
7a83279
Made boto3/botocore optional installs and moved boto3/botocore import…
TimothyWillard Jun 25, 2024
9566d7e
Merge branch 'main' into bug/GH-238-missing-boto3
TimothyWillard Jun 25, 2024
bed8d8b
Change except to only catch ModuleNotFoundError, let other errors raise.
TimothyWillard Jun 27, 2024
58c312c
Add `.env` to `.gitignore`
TimothyWillard Jul 10, 2024
0530231
Merge updates from main into bug/GH-238-missing-boto3
TimothyWillard Jul 11, 2024
df0737d
Merge branch 'main' into bug/GH-238-missing-boto3
TimothyWillard Jul 11, 2024
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8 changes: 6 additions & 2 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ model_output/
/*.Rcheck/

# RStudio files
.Rproj.user/
.Rproj.user
flepiMoP.Rproj
*.Rproj

Expand Down Expand Up @@ -64,7 +64,8 @@ packrat/lib*/
dist/
SEIR.egg-info/
Outcomes.egg-info/
.Rproj.user
venv/
.venv/

# R package manuals
man/
Expand All @@ -74,3 +75,6 @@ flepimop/gempyor_pkg/get_value.prof
flepimop/gempyor_pkg/tests/seir/.coverage
flepimop/gempyor_pkg/tests/seir/.coverage.kojis-mbp-8.sph.ad.jhsph.edu.90615.974746
flepimop/gempyor_pkg/.coverage

# Environment variables
.env
4 changes: 3 additions & 1 deletion flepimop/gempyor_pkg/setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,9 @@ install_requires =
test =
pytest
mock

aws =
boto3
botocore

[options.entry_points]
console_scripts =
Expand Down
13 changes: 9 additions & 4 deletions flepimop/gempyor_pkg/src/gempyor/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,6 @@
import time
from typing import List, Dict, Literal

import boto3
from botocore.exceptions import ClientError
import confuse
import numpy as np
import numpy.typing as npt
Expand Down Expand Up @@ -347,7 +345,7 @@ def as_random_distribution(self):


def list_filenames(
folder: str | bytes | os.PathLike = ".",
folder: str | bytes | os.PathLike = ".",
filters: str | list[str] = [],
) -> list[str]:
"""Return the list of all filenames and paths in the provided folder.
Expand Down Expand Up @@ -636,12 +634,19 @@ def download_file_from_s3(name_map: Dict[str, str]) -> None:
>>> download_file_from_s3(name_map)
# This will raise a ValueError indicating the invalid S3 URI format.
"""
try:
import boto3
from botocore.exceptions import ClientError
except ModuleNotFoundError:
raise ModuleNotFoundError((
"No module named 'boto3', which is required for "
"gempyor.utils.download_file_from_s3. Please install the aws target."
))
s3 = boto3.client("s3")
first_output_filename = next(iter(name_map.values()))
output_dir = os.path.dirname(first_output_filename)
if not os.path.exists(output_dir):
os.makedirs(output_dir)

for s3_uri in name_map:
try:
if s3_uri.startswith("s3://"):
Expand Down
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