Fix ffnet build for Python 3.13+ and mamba 2.x compatibility

CHANGELOG.md

@@ -9,12 +9,34 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- Fix `ffnet` installation for Python 3.13+ and modern pip (26.x):
+  - Remove `--no-use-pep517` flag, which was dropped in pip 23.1
+  - Add `--no-build-isolation` for Python 3.13+ so that `numpy` (required at
+    Fortran compile time) is visible to pip's build backend instead of being
+    hidden inside an isolated sandbox
+  - Simplify misleading echo message in the ffnet install block
+- Remove `--show-channel-urls` flag from `mamba list` calls; the flag is not
+  supported by mamba 2.x and caused the end-of-install package listing to be
+  skipped with a spurious warning
+
 ### Changed
 
+- Update example Python version to 3.14
+- Update example Miniforge version to 26.1.0-0
+- Disable TensorFlow installation for Python 3.14 (see https://github.com/tensorflow/tensorflow/issues/102890)
+
 ### Added
 
+- Explicit Conda Packages
+  - basemap (latest version for Python 3.14 support only on conda-forge)
+- Explicit Pip Packages
+  - python-docx
+
 ### Removed
 
+- Explicit Pip Packages
+  - basemap (latest version for Python 3.14 support only on conda-forge)
+
 ### Deprecated
 
 ## [25.3.1] - 2025-10-02

README.GMAO

@@ -1,5 +1,5 @@
 The command for installing on ford1 is:
 
 ```
-$ ./install_miniconda.bash --python_version 3.12 --miniconda_version 24.5.0-0 --prefix /ford1/share/gmao_SIteam/GEOSpyD
+$ ./install_miniforge.bash --python_version 3.14 --miniforge_version 26.1.0-0 --prefix /ford1/share/gmao_SIteam/GEOSpyD
 ```

README.NAS

@@ -1,5 +1,5 @@
 The command for installing on NAS systems is:
 
 ```
-$ ./install_miniconda.bash --python_version 3.12 --miniconda_version 24.5.0-0 --prefix /nobackup/gmao_SIteam/GEOSpyD
+$ ./install_miniforge.bash --python_version 3.14 --miniforge_version 26.1.0-0 --prefix /nobackup/gmao_SIteam/GEOSpyD
 ```

README.NCCS

@@ -1,5 +1,5 @@
 The command for installing on NCCS system is:
 
 ```
-$ ./install_miniconda.bash --python_version 3.12 --miniconda_version 24.5.0-0 --prefix /usr/local/other/python/GEOSpyD/
+$ ./install_miniforge.bash --python_version 3.14 --miniforge_version 26.1.0-0 --prefix /usr/local/other/python/GEOSpyD/
 ```

README.md

@@ -14,12 +14,12 @@ to prevent infection from the Anaconda `defaults` channel, the script at the end
 In order to use the install script, you can run:
 
 ```
-./install_miniforge.bash --python_version 3.12 --miniforge_version 24.5.0-0 --prefix /opt/GEOSpyD
+./install_miniforge.bash --python_version 3.14 --miniforge_version 26.1.0-0 --prefix /opt/GEOSpyD
 ```
 
 will create an install at:
 ```
-/opt/GEOSpyD/24.5.0-0_py3.12/YYYY-MM-DD
+/opt/GEOSpyD/26.1.0-0/YYYY-MM-DD
 ```
 
 where YYYY-MM-DD is the date of the install. We use a date so that if
@@ -28,17 +28,19 @@ the stack is re-installed, the previous install is not overwritten.
 ## Usage
 
 ```
-Usage: ./install_miniforge.bash --python_version <python version> --miniforge_version <miniforge> --prefix <prefix> [--micromamba | --mamba] [--blas <blas>]
+Usage: ./install_miniforge.bash --python_version <python version> --miniforge_version <miniforge> --prefix <prefix>
+                   [--micromamba | --mamba] [--blas <blas>] [--ffnet-hack]
 
    Required arguments:
-      --python_version <python version> (e.g., 3.12)
-      --miniforge_version <miniforge_version version> (e.g., 24.5.0-0)
+      --python_version <python version> (e.g., 3.14)
+      --miniforge_version <miniforge_version version> (e.g., 26.1.0-0)
       --prefix <full path to installation directory> (e.g, /opt/GEOSpyD)
 
    Optional arguments:
       --blas <blas> (default: accelerate, options: mkl, openblas, accelerate, blis)
       --micromamba: Use micromamba installer (default)
       --mamba: Use mamba installer
+      --ffnet-hack: Install ffnet from fork (used on Bucy due to odd issue not finding gfortran)
       --help: Print this message
 
    By default we use the micromamba installer on both Linux and macOS
@@ -47,17 +49,17 @@ Usage: ./install_miniforge.bash --python_version <python version> --miniforge_ve
    NOTE 1: This script installs within /opt/GEOSpyD with a path based on:
 
         1. The Miniforge version
-        2. The Python version
-        3. The date of the installation
+        2. The date of the installation
 
-   For example: ./install_miniforge.bash --python_version 3.12 --miniforge_version 24.5.0-0 --prefix /opt/GEOSpyD
+   For example: ./install_miniforge.bash --python_version 3.14 --miniforge_version 26.1.0-0 --prefix /opt/GEOSpyD
 
    will create an install at:
-       /opt/GEOSpyD/24.5.0-0_py3.12/2024-08-29
+       /opt/GEOSpyD/26.1.0-0/2026-03-11
 
   NOTE 2: This script will create or substitute a .mambarc
   and .condarc file in the user's home directory.  If you
   have an existing .mambarc and/or .condarc file, it will be
   restored after installation.  We do this to ensure that the
   installation uses conda-forge as the default channel.
 ```
+

install_miniforge.bash

@@ -72,8 +72,8 @@ fi
 # Usage
 # -----
 
-EXAMPLE_PY_VERSION="3.13"
-EXAMPLE_MINI_VERSION="25.3.1-0"
+EXAMPLE_PY_VERSION="3.14"
+EXAMPLE_MINI_VERSION="26.1.0-0"
 EXAMPLE_INSTALLDIR="/opt/GEOSpyD"
 EXAMPLE_DATE=$(date +%F)
 usage() {
@@ -605,6 +605,8 @@ $PACKAGE_INSTALL uxarray
 
 $PACKAGE_INSTALL rasterio contextily
 
+$PACKAGE_INSTALL basemap
+
 # Only install pythran on linux. On mac it brings in an old clang
 if [[ $MINIFORGE_ARCH == Linux ]]
 then
@@ -651,26 +653,34 @@ $PIP_INSTALL PyRTF3 pipenv pymp-pypi h5py
 $PIP_INSTALL pycircleci metpy siphon questionary xgrads
 $PIP_INSTALL ruamel.yaml
 $PIP_INSTALL xgboost
-$PIP_INSTALL tensorflow evidential-deep-learning silence_tensorflow
+
+# Tensorflow does not support Python 3.14 yet
+# https://github.com/tensorflow/tensorflow/issues/102890
+if [[ $PYTHON_VER_WITHOUT_DOT -ge 314 ]]
+then
+   echo "Skipping tensorflow installation as Python $PYTHON_VER is 3.14 or higher"
+else
+   $PIP_INSTALL tensorflow evidential-deep-learning silence_tensorflow
+fi
 $PIP_INSTALL torch
 $PIP_INSTALL yaplon
 $PIP_INSTALL lxml
 $PIP_INSTALL juliandate
 $PIP_INSTALL pybufrkit
 $PIP_INSTALL pyephem
-$PIP_INSTALL basemap
 $PIP_INSTALL redis
 $PIP_INSTALL Flask
 $PIP_INSTALL goes2go
 $PIP_INSTALL nco
 $PIP_INSTALL cdo
 $PIP_INSTALL ecmwf-opendata
+$PIP_INSTALL python-docx
 
 # some packages require a Fortran compiler. This sometimes isn't available
 # on macs (though usually is)
 if [[ $FORTRAN_AVAILABLE == TRUE ]]
 then
-   echo "We have a Fortran compiler and are Python 3.12 or older. Installing ffnet"
+   echo "We have a Fortran compiler. Installing ffnet"
    # we need to install ffnet from https://github.com/mrkwjc/ffnet.git
    # This is because the version in PyPI is not compatible with Python 3
    # and latest scipy
@@ -682,8 +692,14 @@ then
    if [[ $PYTHON_VER_WITHOUT_DOT -ge 313 ]]
    then
       $PIP_INSTALL setuptools wheel
-      # We also need a new flag for Python 3.13
-      EXTRA_PIP_FLAGS='--no-use-pep517'
+   fi
+   # For Python 3.13+, pip's isolated build environment does not inherit the
+   # conda env packages (e.g. numpy), which ffnet needs at build time. Passing
+   # --no-build-isolation tells pip to use the already-installed packages from
+   # the conda env instead of creating a fresh isolated sandbox.
+   if [[ $PYTHON_VER_WITHOUT_DOT -ge 313 ]]
+   then
+      EXTRA_PIP_FLAGS='--no-build-isolation'
    else
       EXTRA_PIP_FLAGS=''
    fi
@@ -755,8 +771,8 @@ $PIP_INSTALL prompt_toolkit
 # Use mamba to output list of packages installed
 # ----------------------------------------------
 cd $MINIFORGE_ENVDIR
-$MINIFORGE_BINDIR/mamba list -n $MINIFORGE_ENVNAME --show-channel-urls --explicit > distribution_spec_file.txt
-$MINIFORGE_BINDIR/mamba list -n $MINIFORGE_ENVNAME --show-channel-urls > mamba_list_packages.txt
+$MINIFORGE_BINDIR/mamba list -n $MINIFORGE_ENVNAME --explicit > distribution_spec_file.txt
+$MINIFORGE_BINDIR/mamba list -n $MINIFORGE_ENVNAME > mamba_list_packages.txt
 ./bin/pip freeze > pip_freeze_packages.txt
 
 # Restore User's .mambarc and .condarc using cleanup function

tests/torch_example.py

@@ -5,8 +5,17 @@
 
 
 dtype = torch.float
-device = torch.device("cpu")
-# device = torch.device("cuda:0") # Uncomment this to run on GPU
+if torch.cuda.is_available():
+    device = torch.device("cuda:0")
+    print(f"Using GPU: {torch.cuda.get_device_name(0)}")
+    print(f"GPU memory allocated: {torch.cuda.memory_allocated(0) / 1024**2:.2f} MB")
+    print(f"GPU memory cached: {torch.cuda.memory_reserved(0) / 1024**2:.2f} MB")
+    print(f"CUDA device count: {torch.cuda.device_count()}")
+    print(f"Current CUDA device: {torch.cuda.current_device()}")
+    print(f"CUDA device name: {torch.cuda.get_device_name(0)}")
+else:
+    device = torch.device("cpu")
+    print("CUDA not available, using CPU")
 
 # Create random input and output data
 x = torch.linspace(-math.pi, math.pi, 2000, device=device, dtype=dtype)

tests/torch_example_like_tflow.py

@@ -0,0 +1,98 @@
+#!/usr/bin/env python3
+
+import torch
+import torch.nn as nn
+import torch.optim as optim
+from torchvision import datasets, transforms
+from torch.utils.data import DataLoader
+
+print("PyTorch version:", torch.__version__)
+print("CUDA available:", torch.cuda.is_available())
+
+# Set device
+device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+print(f"Using device: {device}")
+
+# Load MNIST dataset
+transform = transforms.Compose([
+    transforms.ToTensor(),  # This automatically normalizes to [0, 1]
+])
+
+train_dataset = datasets.MNIST(root='./data', train=True, download=True, transform=transform)
+test_dataset = datasets.MNIST(root='./data', train=False, download=True, transform=transform)
+
+train_loader = DataLoader(train_dataset, batch_size=32, shuffle=True)
+test_loader = DataLoader(test_dataset, batch_size=32, shuffle=False)
+
+# Define the model
+model = nn.Sequential(
+    nn.Flatten(),
+    nn.Linear(28 * 28, 128),
+    nn.ReLU(),
+    nn.Dropout(0.2),
+    nn.Linear(128, 10)
+).to(device)
+
+print(model)
+
+# Loss and optimizer
+criterion = nn.CrossEntropyLoss()  # Combines softmax and negative log likelihood
+optimizer = optim.Adam(model.parameters())
+
+# Training loop
+epochs = 5
+for epoch in range(epochs):
+    model.train()
+    running_loss = 0.0
+    correct = 0
+    total = 0
+
+    for batch_idx, (data, target) in enumerate(train_loader):
+        data, target = data.to(device), target.to(device)
+
+        # Zero the gradients
+        optimizer.zero_grad()
+
+        # Forward pass
+        output = model(data)
+        loss = criterion(output, target)
+
+        # Backward pass and optimize
+        loss.backward()
+        optimizer.step()
+
+        # Statistics
+        running_loss += loss.item()
+        _, predicted = torch.max(output.data, 1)
+        total += target.size(0)
+        correct += (predicted == target).sum().item()
+
+    accuracy = 100 * correct / total
+    avg_loss = running_loss / len(train_loader)
+    print(f'Epoch {epoch + 1}/{epochs} - Loss: {avg_loss:.4f}, Accuracy: {accuracy:.2f}%')
+
+# Evaluation
+model.eval()
+correct = 0
+total = 0
+
+with torch.no_grad():
+    for data, target in test_loader:
+        data, target = data.to(device), target.to(device)
+        output = model(data)
+        _, predicted = torch.max(output.data, 1)
+        total += target.size(0)
+        correct += (predicted == target).sum().item()
+
+test_accuracy = 100 * correct / total
+print(f'\nTest Accuracy: {test_accuracy:.2f}%')
+
+# Get probabilities for first 5 test samples
+model.eval()
+with torch.no_grad():
+    test_data, _ = next(iter(test_loader))
+    test_data = test_data[:5].to(device)
+    logits = model(test_data)
+    probabilities = torch.softmax(logits, dim=1)
+    print("\nProbabilities for first 5 test samples:")
+    print(probabilities)