Makefile initial installation (#630)

CONTRIBUTING.md

@@ -29,6 +29,7 @@ be reported by CoverAlls.
 
 ### Setup
 
+#### With `mamba`
 Clone the git repo and create a `mamba` environment (see how to install `mamba` in the [mamba documentation](https://mamba.readthedocs.io/en/latest/)):
 
 ```bash
@@ -38,6 +39,15 @@ mamba env create -f dev-environment.yml  # Add '-n custom_name' if you want.
 mamba activate xdem-dev  # Or any other name specified above
 ```
 
+#### With `pip`
+```bash
+git clone https://github.com/GlacioHack/xdem.git
+cd xdem
+make install
+```
+
+Please note: pip installation is currently only possible under python3.10.
+
 ### Tests
 
 At least one test per feature (in the associated `tests/test_*.py` file) should be included in the PR, using `pytest` (see existing tests for examples).

Makefile

@@ -0,0 +1,112 @@
+# Autodocumented Makefile for xDEM
+# see: https://marmelab.com/blog/2016/02/29/auto-documented-makefile.html
+# Dependencies : python3 venv
+
+############### GLOBAL VARIABLES ######################
+.DEFAULT_GOAL := help
+SHELL := /bin/bash
+
+# Virtualenv directory name (can be overridden)
+ifndef VENV
+	VENV = "venv"
+endif
+
+# Python version requirement
+PYTHON_VERSION_REQUIRED = 3.10
+
+ifndef PYTHON
+	# Try to find python version required
+	PYTHON = "python$(PYTHON_VERSION_REQUIRED)"
+endif
+PYTHON_CMD=$(shell command -v $(PYTHON))
+
+PYTHON_VERSION_CUR=$(shell $(PYTHON_CMD) -c 'import sys; print("%d.%d" % sys.version_info[0:2])')
+PYTHON_VERSION_OK=$(shell $(PYTHON_CMD) -c 'import sys; req_ver = tuple(map(int, "$(PYTHON_VERSION_REQUIRED)".split("."))); cur_ver = sys.version_info[0:2]; print(int(cur_ver == req_ver))')
+
+############### Check python version supported ############
+
+ifeq (, $(PYTHON_CMD))
+    $(error "PYTHON_CMD=$(PYTHON_CMD) not found in $(PATH)")
+endif
+
+ifeq ($(PYTHON_VERSION_OK), 0)
+    $(error "Requires Python version == $(PYTHON_VERSION_REQUIRED). Current version is $(PYTHON_VERSION_CUR)")
+endif
+
+################ MAKE Targets ######################
+
+help: ## Show this help
+	@echo "      XDEM MAKE HELP"
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
+
+.PHONY: venv
+venv: ## Create a virtual environment in 'venv' directory if it doesn't exist
+	@test -d ${VENV} || $(PYTHON_CMD) -m venv ${VENV}
+	@touch ${VENV}/bin/activate
+	@${VENV}/bin/python -m pip install --upgrade wheel setuptools pip
+
+.PHONY: install-gdal
+install-gdal: ## Install GDAL version matching the system's GDAL via pip
+	@if command -v gdalinfo >/dev/null 2>&1; then \
+		GDAL_VERSION=$$(gdalinfo --version | awk '{print $$2}'); \
+		echo "System GDAL version: $$GDAL_VERSION"; \
+		${VENV}/bin/pip install gdal==$$GDAL_VERSION; \
+	else \
+		echo "Warning: GDAL not found on the system. Proceeding without GDAL."; \
+		echo "Try installing GDAL by running the following commands depending on your system:"; \
+		echo "Debian/Ubuntu: sudo apt-get install -y gdal-bin libgdal-dev"; \
+		echo "Red Hat/CentOS: sudo yum install -y gdal gdal-devel"; \
+		echo "Then run 'make install-gdal' to proceed with GDAL installation."; \
+	fi
+
+.PHONY: install
+install: venv ## Install xDEM for development (depends on venv)
+	@test -f ${VENV}/bin/xdem || echo "Installing xdem in development mode"
+	@test -f ${VENV}/bin/xdem || ${VENV}/bin/pip install -e .[dev]
+	@test -f .git/hooks/pre-commit || echo "Installing pre-commit hooks"
+	@test -f .git/hooks/pre-commit || ${VENV}/bin/pre-commit install -t pre-commit
+	@test -f .git/hooks/pre-push || ${VENV}/bin/pre-commit install -t pre-push
+	@echo "Attempting to install GDAL..."
+	@make install-gdal
+	@echo "xdem installed in development mode in virtualenv ${VENV}"
+	@echo "To use: source ${VENV}/bin/activate; xdem -h"
+
+
+.PHONY: test
+test: ## run tests
+	@if ! ${VENV}/bin/python -m pip show gdal >/dev/null 2>&1; then \
+		echo "Error: GDAL is not installed in the virtual environment. Tests require GDAL to run."; \
+		echo "Please ensure GDAL is installed by running 'make install-gdal'."; \
+		exit 1; \
+	else \
+		${VENV}/bin/pytest; \
+	fi
+
+## Clean section
+
+.PHONY: clean
+clean: clean-venv clean-build clean-pyc clean-precommit ## Clean all
+
+.PHONY: clean-venv
+clean-venv: ## Clean the virtual environment
+	@echo "+ $@"
+	@rm -rf ${VENV}
+
+.PHONY: clean-build
+clean-build: ## Remove build artifacts
+	@echo "+ $@"
+	@rm -rf build/ dist/ .eggs/
+	@find . -name '*.egg-info' -exec rm -rf {} +
+	@find . -name '*.egg' -exec rm -f {} +
+
+.PHONY: clean-precommit
+clean-precommit: ## Remove pre-commit hooks from .git/hooks
+	@rm -f .git/hooks/pre-commit
+	@rm -f .git/hooks/pre-push
+
+.PHONY: clean-pyc
+clean-pyc: ## Remove Python cache and artifacts
+	@echo "+ $@"
+	@find . -type f -name "*.py[co]" -exec rm -rf {} +
+	@find . -type d -name "__pycache__" -exec rm -rf {} +
+	@find . -name '*~' -exec rm -rf {} +

README.md

@@ -40,11 +40,19 @@ For a quick start, full feature description or search through the API, see xDEM'
 
 ## Installation
 
+### With `mamba`
+
 ```bash
 mamba install -c conda-forge xdem
 ```
 See [mamba's documentation](https://mamba.readthedocs.io/en/latest/) to install `mamba`, which will solve your environment much faster than `conda`.
 
+### With `pip`
+
+```bash
+pip install xdem
+```
+
 ## Citing methods implemented in the package
 
 When using a method implemented in xDEM, please **cite both the package and the related study**:

dev-environment.yml

@@ -14,12 +14,18 @@ dependencies:
   - scikit-image=0.*
   - scikit-gstat>=1.0.18,<1.1
   - geoutils=0.1.12
+  - affine
+  - pandas
+  - pyogrio
+  - shapely
 
   # Development-specific, to mirror manually in setup.cfg [options.extras_require].
   - pip
 
   # Optional dependencies
   - pytransform3d
+  - pyyaml
+  - scikit-learn
 
   # Test dependencies
   - gdal  # To test against GDAL
@@ -28,7 +34,7 @@ dependencies:
   - pyyaml
   - flake8
   - pylint
-  - richdem
+  - richdem # To test against richdem
 
   # Doc dependencies
   - sphinx
@@ -47,6 +53,7 @@ dependencies:
     # Optional dependency
     - -e ./
 
+    - noisyopt
     # "Headless" needed for opencv to install without requiring system dependencies
     - opencv-contrib-python-headless
 

doc/source/how_to_install.md

@@ -28,9 +28,20 @@ Updating packages with `pip` (and sometimes `mamba`) can break your installation
 
 ## Installing for contributors
 
+### With ``mamba``
+
 ```bash
 git clone https://github.com/GlacioHack/xdem.git
 mamba env create -f xdem/dev-environment.yml
 ```
 
+### With ``pip``
+
+Please note: pip installation is currently only possible under python3.10.
+
+```bash
+git clone https://github.com/GlacioHack/xdem.git
+make install
+```
+
 After installing, you can check that everything is working by running the tests: `pytest`.

environment.yml

@@ -15,6 +15,10 @@ dependencies:
   - scikit-gstat>=1.0.18,<1.1
   - geoutils=0.1.12
   - pip
+  - affine
+  - pandas
+  - pyogrio
+  - shapely
 
    # To run CI against latest GeoUtils
 #  - pip:

requirements.txt

@@ -13,3 +13,7 @@ scikit-image==0.*
 scikit-gstat>=1.0.18,<1.1
 geoutils==0.1.12
 pip
+affine
+pandas
+pyogrio
+shapely

setup.cfg

@@ -49,16 +49,18 @@ include =
 
 [options.extras_require]
 opt =
-    opencv
-    openh264
+    opencv-contrib-python-headless
     pytransform3d
     noisyopt
+    scikit-learn
+    pyyaml
 test =
     pytest
     pytest-xdist
-    pyyaml
+    pre-commit
     flake8
     pylint
+    scikit-learn
     richdem
 doc =
     sphinx
@@ -73,7 +75,7 @@ doc =
     numpydoc
 dev =
     %(opt)s
-    %(test)s
     %(doc)s
+    %(test)s
 all =
     %(dev)s