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21 changes: 21 additions & 0 deletions .vscode/launch.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
{
"version": "0.2.0",
"configurations": [
{
"name": "Run model.py",
"type": "debugpy",
"request": "launch",
"program": "${workspaceFolder}/src/model.py",
"console": "integratedTerminal",
"python": "${command:python.interpreterPath}"
},
{
"name": "Run model2.py",
"type": "debugpy",
"request": "launch",
"program": "${workspaceFolder}/src/model2.py",
"console": "integratedTerminal",
"python": "${command:python.interpreterPath}"
}
]
}
142 changes: 5 additions & 137 deletions src/helloworldPy.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,141 +2,9 @@ name: helloworldPy
channels:
- conda-forge
- defaults
- https://repo.anaconda.com/pkgs/main
- https://repo.anaconda.com/pkgs/r
- https://repo.anaconda.com/pkgs/msys2
dependencies:
- affine=2.4.0=pyhd8ed1ab_1
- attrs=24.3.0=pyh71513ae_0
- aws-c-auth=0.7.20=h6823eb1_0
- aws-c-cal=0.6.12=hc83774a_0
- aws-c-common=0.9.17=h2466b09_0
- aws-c-compression=0.2.18=hc83774a_4
- aws-c-event-stream=0.4.2=hc6c0aac_10
- aws-c-http=0.8.1=hced5053_13
- aws-c-io=0.14.8=hebaacdb_0
- aws-c-mqtt=0.10.4=hdafd9a4_2
- aws-c-s3=0.5.9=h7a83f0e_0
- aws-c-sdkutils=0.1.16=hc83774a_0
- aws-checksums=0.1.18=hc83774a_4
- aws-crt-cpp=0.26.8=h672a689_11
- aws-sdk-cpp=1.11.267=h12f3f85_8
- azure-core-cpp=1.11.1=h249a519_1
- azure-storage-blobs-cpp=12.10.0=h91493d7_1
- azure-storage-common-cpp=12.5.0=h91493d7_4
- blosc=1.21.6=h85f69ea_0
- bzip2=1.0.8=h2466b09_7
- c-ares=1.34.4=h2466b09_0
- ca-certificates=2024.12.14=h56e8100_0
- cairo=1.18.0=h91e5215_2
- certifi=2024.12.14=pyhd8ed1ab_0
- cfitsio=4.4.0=h9b0cee5_1
- click=8.1.8=pyh7428d3b_0
- click-plugins=1.1.1=pyhd8ed1ab_1
- cligj=0.7.2=pyhd8ed1ab_2
- colorama=0.4.6=pyhd8ed1ab_1
- fmt=10.2.1=h181d51b_0
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=h77eed37_3
- fontconfig=2.15.0=h765892d_1
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- freetype=2.12.1=hdaf720e_2
- freexl=2.0.0=hf297d47_2
- gdal=3.7.3=py310h7028bf2_20
- geos=3.12.1=h1537add_0
- geotiff=1.7.1=hbf5ca3a_15
- hdf4=4.2.15=h5557f11_7
- hdf5=1.14.3=nompi_hd5d9e70_108
- icu=73.2=h63175ca_0
- intel-openmp=2024.2.1=h57928b3_1083
- kealib=1.5.3=h6c43f9b_2
- krb5=1.21.3=hdf4eb48_0
- lcms2=2.16=h67d730c_0
- lerc=4.0.0=h63175ca_0
- libabseil=20240116.2=cxx17_he0c23c2_1
- libaec=1.1.3=h63175ca_0
- libarchive=3.7.7=h88ece9c_0
- libblas=3.9.0=26_win64_mkl
- libcblas=3.9.0=26_win64_mkl
- libcrc32c=1.1.2=h0e60522_0
- libcurl=8.11.1=h88aaa65_0
- libdeflate=1.20=hcfcfb64_0
- libexpat=2.6.4=he0c23c2_0
- libffi=3.4.2=h8ffe710_5
- libgdal=3.7.3=h1fd769a_20
- libglib=2.80.2=h0df6a38_0
- libgoogle-cloud=2.23.0=h68df31e_1
- libgoogle-cloud-storage=2.23.0=hb581fae_1
- libgrpc=1.62.2=h5273850_0
- libhwloc=2.11.2=default_ha69328c_1001
- libiconv=1.17=hcfcfb64_2
- libintl=0.22.5=h5728263_3
- libjpeg-turbo=3.0.0=hcfcfb64_1
- libkml=1.3.0=h538826c_1021
- liblapack=3.9.0=26_win64_mkl
- liblzma=5.6.3=h2466b09_1
- liblzma-devel=5.6.3=h2466b09_1
- libnetcdf=4.9.2=nompi_h008f77d_116
- libpng=1.6.44=h3ca93ac_0
- libpq=16.6=h5b74ccd_1
- libprotobuf=4.25.3=h47a098d_1
- libre2-11=2023.09.01=hf8d8778_2
- librttopo=1.1.0=h94c4f80_15
- libspatialite=5.1.0=hf2f0abc_4
- libsqlite=3.47.2=h67fdade_0
- libssh2=1.11.1=he619c9f_0
- libtiff=4.6.0=hddb2be6_3
- libwebp-base=1.5.0=h3b0e114_0
- libwinpthread=12.0.0.r4.gg4f2fc60ca=h57928b3_8
- libxml2=2.13.5=he286e8c_1
- libzip=1.11.2=h3135430_0
- libzlib=1.3.1=h2466b09_2
- lz4-c=1.9.4=hcfcfb64_0
- lzo=2.10=hcfcfb64_1001
- minizip=4.0.7=h9fa1bad_3
- mkl=2024.2.2=h66d3029_15
- numpy=1.26.4=py310hf667824_0
- openjpeg=2.5.2=h3d672ee_0
- openssl=3.4.0=h2466b09_0
- pandas=2.2.3=py310hb4db72f_1
- pcre2=10.43=h17e33f8_0
- pip=24.3.1=pyh8b19718_2
- pixman=0.44.2=had0cd8c_0
- poppler=24.03.0=hc2f3c52_0
- poppler-data=0.4.12=hd8ed1ab_0
- postgresql=16.6=h5b59834_1
- proj=9.3.1=he13c7e8_0
- pyparsing=3.2.1=pyhd8ed1ab_0
- pysyncrosim=2.0.1=pyhecae5ae_0
- python=3.10.16=h37870fc_1_cpython
- python-dateutil=2.9.0.post0=pyhff2d567_1
- python-tzdata=2024.2=pyhd8ed1ab_1
- python_abi=3.10=5_cp310
- pytz=2024.1=pyhd8ed1ab_0
- rasterio=1.3.9=py310h8ed2791_1
- re2=2023.09.01=hd3b24a8_2
- setuptools=75.6.0=pyhff2d567_1
- six=1.17.0=pyhd8ed1ab_0
- snappy=1.2.1=h500f7fa_1
- snuggs=1.4.7=pyhd8ed1ab_2
- spdlog=1.13.0=h64d2f7d_0
- sqlite=3.47.2=h2466b09_0
- tbb=2021.13.0=h62715c5_1
- tiledb=2.21.2=hf39fa12_4
- tk=8.6.13=h5226925_1
- tzdata=2024b=hc8b5060_0
- ucrt=10.0.22621.0=h57928b3_1
- uriparser=0.9.8=h5a68840_0
- vc=14.3=ha32ba9b_23
- vc14_runtime=14.42.34433=he29a5d6_23
- vs2015_runtime=14.42.34433=hdffcdeb_23
- wheel=0.45.1=pyhd8ed1ab_1
- xerces-c=3.2.5=he0c23c2_2
- xz=5.6.3=h208afaa_1
- xz-tools=5.6.3=h2466b09_1
- zlib=1.3.1=h2466b09_2
- zstd=1.5.6=h0ea2cb4_0
prefix: C:\Users\DorianaRomualdi\miniconda3\envs\helloworldPy
- pysyncrosim=2.1.3
- numpy=2.3.5
- pandas=2.3.3
- gdal=3.10.3
- rasterio=1.4.3
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⚠️ Potential issue | 🟠 Major

🧩 Analysis chain

🏁 Script executed:

# Find and examine the conda environment file
fd -t f 'helloworldPy.yml' 

# Check if the file exists and view its current content
if [ -f "src/helloworldPy.yml" ]; then
  echo "=== Current content of src/helloworldPy.yml ==="
  cat -n src/helloworldPy.yml
fi

Repository: ApexRMS/helloworldSpatialPy

Length of output: 371


🏁 Script executed:

# Check for Python imports in the model files mentioned
if [ -f "src/model.py" ]; then
  echo "=== src/model.py ==="
  cat -n src/model.py
fi

if [ -f "src/model2.py" ]; then
  echo "=== src/model2.py ==="
  cat -n src/model2.py
fi

Repository: ApexRMS/helloworldSpatialPy

Length of output: 5616


🏁 Script executed:

# Search for any documentation or references to pysyncrosim version requirements
rg 'pysyncrosim|python.*version|Python.*3\.' --max-count=20

Repository: ApexRMS/helloworldSpatialPy

Length of output: 190


🏁 Script executed:

# Check if there are any other conda environment files or related configs
fd -t f '\.(yml|yaml)$' | grep -E '(conda|env|environment)'

Repository: ApexRMS/helloworldSpatialPy

Length of output: 53


🌐 Web query:

pysyncrosim 2.1.3 Python version requirements

💡 Result:

PySyncroSim 2.1.3 does not declare a strict Requires-Python constraint on PyPI (the metadata field is null), but it is published as a Python 3 wheel (py3-none-any). [1]

The project’s own install docs state it was tested and developed with Python 3.12 (along with SyncroSim 3.0.9), and their example conda environment uses python=3.12. [2]

Practical takeaway: use Python 3.12 (recommended/known-good); at minimum you need Python 3. [1] [2]

Sources
[1] PyPI JSON metadata for pysyncrosim==2.1.3 (requires_python, wheel tag) (pypi.org)
[2] PySyncroSim 2.1.3 installation documentation (tested/developed with Python 3.12) (pysyncrosim.readthedocs.io)

Citations:


🌐 Web query:

SyncroSim conda environment Python version documentation

💡 Result:

SyncroSim’s documentation covers Python versioning for package-specific conda environments here:

  • “Adding conda environments” (SyncroSim dev docs): shows creating an environment with an explicit Python version, e.g. conda create -n new_env python=3.10, and also installing Python into the env with conda install python=3.10. It then explains exporting the env to a .yml and referencing it from package.xml via condaEnv / condaEnvVersion. [1]

  • “Using Conda” (SyncroSim how-to guide): explains that SyncroSim conda environments can include “correct versions of software such as R and Python,” and that SyncroSim can prompt users to create the package’s conda environment at install time. [2]

Sources: [1], [2]


🏁 Script executed:

# Check for package.xml or other config files that might reference Python
fd -t f 'package\.xml' 
if [ -f "src/package.xml" ]; then
  echo "=== src/package.xml ==="
  cat -n src/package.xml
fi

Repository: ApexRMS/helloworldSpatialPy

Length of output: 3476


🏁 Script executed:

# Look for any README or documentation in the repo
fd -t f '\.(md|txt|rst)$' | head -20
cat README.md 2>/dev/null | head -100

Repository: ApexRMS/helloworldSpatialPy

Length of output: 168


Pin python explicitly in this conda environment file.

This file defines the exact runtime environment for both transformers in package.xml. Without an explicit Python version pin, the conda solver can select any Python 3.x release when installing or updating the environment, risking different behaviour than documented. The official pysyncrosim documentation explicitly states the package was tested and developed with Python 3.12, and their own example conda environments include an explicit python=3.12 pin. SyncroSim's conda documentation emphasizes that environment YAML files should specify exact versions of software dependencies, including Python.

Add python=3.12 (or the version you have validated) to ensure future installs use the same interpreter version this package was tested against:

Suggested change
 dependencies:
+  - python=3.12
   - pysyncrosim=2.1.3
   - numpy=2.3.5
   - pandas=2.3.3
   - gdal=3.10.3
   - rasterio=1.4.3
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
- pysyncrosim=2.1.3
- numpy=2.3.5
- pandas=2.3.3
- gdal=3.10.3
- rasterio=1.4.3
dependencies:
- python=3.12
- pysyncrosim=2.1.3
- numpy=2.3.5
- pandas=2.3.3
- gdal=3.10.3
- rasterio=1.4.3
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/helloworldPy.yml` around lines 6 - 10, The conda environment YAML is
missing an explicit Python version, which can lead the resolver to pick varying
Python 3.x interpreters; update the environment definition that lists packages
like pysyncrosim, numpy, pandas, gdal, and rasterio to add an explicit
python=3.12 entry so installs use the tested interpreter (e.g., add
"python=3.12" alongside the existing package pins in the same top-level
dependencies list).

19 changes: 11 additions & 8 deletions src/model.py
Original file line number Diff line number Diff line change
Expand Up @@ -20,26 +20,29 @@
# Load Run Control Datasheet to set timesteps
run_settings = myScenario.datasheets(name="helloworldSpatialPy_RunControl")


# Set timesteps
timesteps = np.array(range(run_settings.MinimumTimestep.item(),
run_settings.MaximumTimestep.item() + 1))

# Load Scenario's input Datasheet from SyncroSim Library into DataFrame
my_input_dataframe = myScenario.datasheets(name="helloworldSpatialPy_InputDatasheet")
my_input_dataframe = myScenario.datasheets(
name="helloworldSpatialPy_InputDatasheet",
show_full_paths=True)

# Extract model inputs from Input DataFrame
m_mean = my_input_dataframe.mMean.item()
m_sd = my_input_dataframe.mSD.item()

# Load raster input
raster_map = myScenario.datasheet_rasters(datasheet="helloworldSpatialPy_InputDatasheet",
column="InterceptRasterFile")
raster_values = raster_map.values()
raster_path = my_input_dataframe.InterceptRasterFile.item()
with rasterio.open(raster_path) as src:
raster_values = src.read(1)
raster_crs = src.crs

# Set up empty pandas DataFrame to accept output values
my_output_dataframe = myScenario.datasheets(name="helloworldSpatialPy_IntermediateDatasheet",
empty=True)
my_output_dataframe = myScenario.datasheets(
name="helloworldSpatialPy_IntermediateDatasheet",
empty=True)

# For loop through iterations
for i in range(1, run_settings.MaximumIteration.item() + 1):
Expand All @@ -61,7 +64,7 @@
height=raster_values.shape[0],
width=raster_values.shape[1],
count=1, dtype=raster_values.dtype,
crs=raster_map.crs) as infile:
crs=raster_crs) as infile:
infile.write(new_raster_list[ts], indexes=1)
filename_list.append(filename)

Expand Down
6 changes: 3 additions & 3 deletions src/package.xml
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="utf-8"?>
<package name="helloworldSpatialPy" displayName="Hello World Spatial (Python)" description="Example demonstrating how to use spatial data with a Python model" version="2.0.0" url="https://apexrms.github.io/helloworldEnhanced/">
<package name="helloworldSpatialPy" displayName="Hello World Spatial (Python)" description="Example demonstrating how to use spatial data with a Python model" version="2.2.0" url="https://apexrms.github.io/helloworldEnhanced/">

<!--Scenario Datasheets-->

Expand Down Expand Up @@ -28,14 +28,14 @@
<!--Transformers-->

<!--First Transformer-->
<transformer name="firstModel" displayName="Hello World Spatial 1 (Python)" programArguments="model.py" condaEnv="helloworldPy.yml" condaEnvVersion="1">
<transformer name="firstModel" displayName="Hello World Spatial 1 (Python)" programArguments="model.py" condaEnv="helloworldPy.yml" condaEnvVersion="2">
<dataSheet name="RunControl" type="Input"/>
<dataSheet name="InputDatasheet" type="Input"/>
<dataSheet name="IntermediateDatasheet" type="Output"/>
</transformer>

<!--Second Transformer-->
<transformer name="secondModel" displayName="Hello World Spatial 2 (Python)" programArguments="model2.py" condaEnv="helloworldPy.yml" condaEnvVersion="1">
<transformer name="secondModel" displayName="Hello World Spatial 2 (Python)" programArguments="model2.py" condaEnv="helloworldPy.yml" condaEnvVersion="2">
<dataSheet name="RunControl" type="Input"/>
<dataSheet name="IntermediateDatasheet" type="Input"/>
<dataSheet name="OutputDatasheet" type="Output"/>
Expand Down