Readme update and locally MacOS test (install from repo)

README.md

@@ -12,7 +12,7 @@ Xiaohang Yu, Ti Wang, Mackenzie Weygandt Mathis
 ---
 
 
-## 🚀 TL;DR
+## TL;DR
 PRIMA creates a 3D quadruped mesh from a single 2D image. It leverages BioCLIP-based biological priors for robust cross-species shape understanding, then applies test-time adaptation with 2D reprojection and auxiliary keypoint guidance to refine SMAL pose and shape predictions. 
 
 It further can be used to build Quadruped3D, a large-scale pseudo-3D dataset with diverse species and poses. 
@@ -21,15 +21,19 @@ PRIMA achieves state-of-the-art results on Animal3D, CtrlAni3D, Quadruped2D, and
 
 ## Installation
 
+PRIMA requires Python 3.10 or newer. A CUDA-enabled PyTorch installation is
+recommended for local inference and training.
+
 ### Install from PyPI
 
-> Recommended: Python 3.10 and a CUDA-enabled PyTorch installation.
+Create a clean environment, install PyTorch for your CUDA version, then install
+the package:
 
 ```bash
 conda create -n prima python=3.10 -y
 conda activate prima
 
-# Install PyTorch matching your CUDA (example: CUDA 11.8)
+# Example for CUDA 11.8. Adjust this command for your CUDA version.
 pip install --index-url https://download.pytorch.org/whl/cu118 \
     "torch==2.2.1" "torchvision==0.17.1" "torchaudio==2.2.1"
 
@@ -39,48 +43,60 @@ python -m pip install --no-build-isolation \
 python -m pip install --no-build-isolation \
       "git+https://github.com/facebookresearch/pytorch3d.git"
 
+# Install PRIMA from PyPI-test (for now)
+pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple prima-animal==0.1.7
+
 # Install PRIMA from PyPI
 pip install prima-animal
 ```
 
 `prima-animal` includes demo runtime dependencies used by `demo.py`, `demo_tta.py`, and `app.py` (including Detectron2 and DeepLabCut).
 
-### Clean install from this repository
+### Install from this repository
+
+Use this path if you want to run the code from a fresh clone.
+
+```bash
+git clone https://github.com/AdaptiveMotorControlLab/PRIMA.git
+cd PRIMA
+```
 
-Use these when developing from a **git clone** (not the PyPI wheel). The shell scripts are **non-interactive** (pip uses `--no-input`; `GIT_TERMINAL_PROMPT=0` for git). Put Hugging Face credentials in your environment or git credential helper before pushing the Space.
+The helper script below creates a fresh virtual environment, installs runtime
+dependencies, pulls Git LFS assets if available, downloads the default demo
+checkpoints/data, and verifies that the demo dependencies can be imported:
 
-**Local (fresh venv, LFS assets, Hub demo weights, smoke test)** — requires **Python 3.10+**
-(Gradio 5.1+ / Space-provided Gradio 6.x and `app.py` type hints). On macOS without `python3.10` on your `PATH`, install
-`brew install python@3.10` and set `PRIMA_PYTHON=/opt/homebrew/bin/python3.10`.
 
 ```bash
-chmod +x scripts/clean_install_local.sh scripts/clean_redeploy_hf_space.sh scripts/deploy_hf_space.sh
-PRIMA_PYTHON=/opt/homebrew/bin/python3.10 ./scripts/clean_install_local.sh
+PRIMA_PYTHON=/path/to/python3.10 \
+PRIMA_VENV=prima_env \
+./scripts/clean_install_local.sh
+source prima_env/bin/activate
 ```
 
 Options:
 
-- `PRIMA_VENV=.venv ./scripts/clean_install_local.sh --skip-data` — skip the large `setup_demo_data` download if `data/` is already populated.
-- `./scripts/clean_install_local.sh --wipe-data --force-data` — delete downloaded `data/` assets and redownload.
-- `./scripts/clean_install_local.sh --no-editable` — only `requirements.txt` (no `pip install -e .`); use if editable install fails and you will install the training stack via conda as in the PyPI section above. You still need **Python 3.10+** for Gradio 5.1+. The smoke test sets `PYTHONPATH` to the repo root so `import prima` works without an editable install.
-- **macOS / DeepLabCut:** `requirements.txt` pins `deeplabcut==3.0.0rc14`
-  for the SuperAnimal PyTorch API. On macOS, `clean_install_local.sh` installs
-  it separately after a compatible PyTables wheel (`tables>=3.9.2,<3.11`) to
-  avoid Apple Silicon build issues. Validate the local setup with
-  `./scripts/test_local_full.sh`.
+- `--skip-data` skips the large demo data download if `data/` is already populated.
+- `--wipe-data --force-data` removes downloaded demo assets and downloads them again.
+- `--no-editable` installs dependencies without registering the repo as an editable package.
 
-After `requirements.txt`, the script runs **`pip install --no-deps -e .`** so the `prima` package is registered without re-resolving `pyproject.toml` (which would pull **Detectron2** from git again). Install Detectron2 separately if needed: `pip install 'git+https://github.com/facebookresearch/detectron2.git'`.
+On macOS, install Python 3.10 if needed:
 
-**Hugging Face Space (full redeploy from your working tree):**
+```bash
+brew install python@3.10
+PRIMA_PYTHON=/opt/homebrew/bin/python3.10 \
+PRIMA_VENV=prima_env \
+./scripts/clean_install_local.sh
+source prima_env/bin/activate
+```
 
-Requires [Git LFS / Xet](https://huggingface.co/docs/hub/xet/using-xet-storage#git) tooling (`brew install git-lfs git-xet`, `git xet install`, `git lfs install`). Then:
+If macOS reports `Cannot read image: demo_data/...`, install Git LFS and pull
+the demo images:
 
 ```bash
-./scripts/clean_redeploy_hf_space.sh
+git lfs install
+git lfs pull --include="demo_data/*"
 ```
 
-This is equivalent to `./scripts/deploy_hf_space.sh` and force-pushes a fresh snapshot to the Space.
-
 ---
 
 ## Demo
@@ -170,32 +186,6 @@ The `s1ckpt_inference.ckpt` checkpoint is downloaded automatically if missing.
 
 Override for testing: `PRIMA_DEMO_MODE=local` or `PRIMA_DEMO_MODE=space`.
 
-#### Hugging Face Space (maintainers)
-
-Demo images under `demo_data/` and `images/teaser.png` are tracked with **Git LFS**
-(see `.gitattributes`) so they can be pushed to a Hugging Face Space under the Hub’s
-LFS / **Xet** bridge. Install tooling once:
-
-```bash
-brew install git-lfs git-xet
-git xet install
-git lfs install
-```
-
-Then from a clean checkout with LFS files present, redeploy the Space (same as `clean_redeploy_hf_space.sh`):
-
-```bash
-./scripts/deploy_hf_space.sh
-# or
-./scripts/clean_redeploy_hf_space.sh
-```
-
-The script rsyncs only the Git-tracked files needed by the Space from the
-working tree (not `git archive`) so image files are materialized before
-`git add` turns them into LFS blobs.
-During deployment, `detectron2` is removed from the Space `requirements.txt`;
-the app uses the DeepLabCut SuperAnimal detector fallback on the CPU Space.
-
 ---
 
 

scripts/clean_install_local.sh

@@ -68,29 +68,69 @@ resolve_python() {
     return 1
   fi
   local c p
-  for c in python3.12 python3.11 python3.10; do
+  for c in python3.10 python3.11; do
     if command -v "$c" >/dev/null 2>&1; then
       if "$c" -c 'import sys; raise SystemExit(0 if sys.version_info >= (3, 10) else 1)'; then
         command -v "$c"
         return 0
       fi
     fi
   done
-  for p in /opt/homebrew/bin/python3.10 /usr/local/bin/python3.10; do
+  for p in /opt/homebrew/bin/python3.10 /usr/local/bin/python3.10 /opt/homebrew/opt/python@3.10/bin/python3.10 /usr/local/opt/python@3.10/bin/python3.10; do
     if [[ -x "$p" ]]; then
       echo "$p"
       return 0
     fi
   done
+  if command -v python3.12 >/dev/null 2>&1; then
+    command -v python3.12
+    return 0
+  fi
+  return 1
+}
+
+resolve_torch_index_url() {
+  if [[ -n "${PRIMA_TORCH_INDEX_URL:-}" ]]; then
+    echo "${PRIMA_TORCH_INDEX_URL}"
+    return 0
+  fi
+
+  if [[ "$(uname -s)" == "Darwin" ]]; then
+    return 1
+  fi
+
+  if command -v nvcc >/dev/null 2>&1; then
+    local cuda_version
+    cuda_version="$(nvcc --version | sed -n 's/.*release \([0-9][0-9]*\.[0-9][0-9]*\).*/\1/p' | head -n 1)"
+    case "${cuda_version}" in
+      11.8)
+        echo "https://download.pytorch.org/whl/cu118"
+        return 0
+        ;;
+      12.1)
+        echo "https://download.pytorch.org/whl/cu121"
+        return 0
+        ;;
+      "")
+        echo "[clean-install] WARN: Could not parse nvcc CUDA version; using pip default PyTorch wheel." >&2
+        return 1
+        ;;
+      *)
+        echo "[clean-install] WARN: CUDA ${cuda_version} detected; set PRIMA_TORCH_INDEX_URL if Detectron2 needs a specific PyTorch wheel." >&2
+        return 1
+        ;;
+    esac
+  fi
+
   return 1
 }
 
 echo "[clean-install] Repository: ${ROOT}"
 
 if ! PY="$(resolve_python)"; then
-  echo "[clean-install] ERROR: Need Python 3.10 or newer (Gradio 5 + app type hints)." >&2
-  echo "  macOS: brew install python@3.10" >&2
-  echo "  Then: PRIMA_PYTHON=/opt/homebrew/bin/python3.10 $0 ..." >&2
+  echo "[clean-install] ERROR: Need Python 3.10, 3.11, or 3.12 on PATH, or set PRIMA_PYTHON." >&2
+  echo "  Conda example: PRIMA_PYTHON=\$HOME/miniconda3/envs/prima/bin/python3.10 $0 ..." >&2
+  echo "  macOS example: brew install python@3.10 && PRIMA_PYTHON=/opt/homebrew/bin/python3.10 $0 ..." >&2
   exit 1
 fi
 echo "[clean-install] Using Python: $("$PY" -c 'import sys; print(sys.executable, sys.version.split()[0])')"
@@ -116,10 +156,20 @@ source "${VENV}/bin/activate"
 python -m pip install --no-input -U pip wheel
 # Match requirements.txt / pyproject pins before pulling the rest
 python -m pip install --no-input "setuptools<81" "packaging<25" "Cython<3"
+python -m pip install --no-input "numpy==1.26.1"
+
+echo "[clean-install] xtcocotools (needs numpy available during build) ..."
+python -m pip install --no-input --no-build-isolation "xtcocotools==1.14.3"
+
+if TORCH_INDEX_URL="$(resolve_torch_index_url)"; then
+  echo "[clean-install] Installing PyTorch from ${TORCH_INDEX_URL} ..."
+  python -m pip install --no-input --index-url "${TORCH_INDEX_URL}" \
+    "torch==2.2.1" "torchvision==0.17.1"
+fi
 
 echo "[clean-install] pip install -r requirements.txt (this can take a long time) ..."
 REQ_TMP="$(mktemp)"
-grep -vE '^[[:space:]]*(deeplabcut|detectron2)' "${ROOT}/requirements.txt" > "${REQ_TMP}"
+grep -vE '^[[:space:]]*(deeplabcut|detectron2|xtcocotools)' "${ROOT}/requirements.txt" > "${REQ_TMP}"
 python -m pip install --no-input -r "${REQ_TMP}"
 rm -f "${REQ_TMP}"
 
@@ -153,12 +203,12 @@ if [[ "$WIPE_DATA" -eq 1 ]]; then
 fi
 
 if [[ "$SKIP_DATA" -eq 0 ]]; then
-  FORCE_ARGS=()
+  echo "[clean-install] Downloading demo assets (large) ..."
   if [[ "$FORCE_DATA" -eq 1 ]]; then
-    FORCE_ARGS=(--force)
+    python "${ROOT}/scripts/setup_demo_data.py" --force
+  else
+    python "${ROOT}/scripts/setup_demo_data.py"
   fi
-  echo "[clean-install] Downloading demo assets (large) ..."
-  python "${ROOT}/scripts/setup_demo_data.py" "${FORCE_ARGS[@]}"
 else
   echo "[clean-install] Skipping setup_demo_data (--skip-data)."
 fi