[build,core,utils] Remove pyyaml, move storage.py to core

BioMedIA · Aug 4, 2023 · 2064f3d · 2064f3d
1 parent b2ac443
commit 2064f3d
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Showing 21 changed files with 3,345 additions and 740 deletions.
diff --git a/conda/Makefile b/conda/Makefile
@@ -4,13 +4,6 @@ NAME = deepali
 # Relative path of repository root directory
 ROOT = ..
 
-# Commands
-CONDA = mamba
-CONDA_OPTS = --no-banner
-CONDA_DEVENV = conda devenv
-CONDA_LOCK = conda-lock
-CONDA_LOCK_OPTS = --mamba
-
 # Name of conda-devenv configuration file
 DEVENV = environment.devenv.yml
 
@@ -66,20 +59,20 @@ clear:
 	@rm -f $(LOCKFILE) environment.devenv.{linux-64,osx-64,win-64}.yml environment.{linux-64,osx-64,win-64}.{lock,yml}
 
 lock-linux:
-	@$(CONDA_DEVENV) --name $(NAME) --file $(DEVENV) --env-manager $(CONDA) --env-var PLATFORM=linux-64 --print > environment.devenv.linux-64.yml
-	@$(CONDA_LOCK) $(CONDA_LOCK_OPTS) --lockfile $(LOCKFILE) --platform linux-64 --file environment.devenv.linux-64.yml
+	conda devenv --name $(NAME) --file $(DEVENV) --env-manager conda --env-var PLATFORM=linux-64 --print > environment.devenv.linux-64.yml
+	conda lock --lockfile $(LOCKFILE) --platform linux-64 --file environment.devenv.linux-64.yml
 
 lock-osx:
-	@$(CONDA_DEVENV) --name $(NAME) --file $(DEVENV) --env-manager $(CONDA) --env-var PLATFORM=osx-64 --print > environment.devenv.osx-64.yml
-	@$(CONDA_LOCK) $(CONDA_LOCK_OPTS) --lockfile $(LOCKFILE) --platform osx-64 --file environment.devenv.osx-64.yml
+	conda devenv --name $(NAME) --file $(DEVENV) --env-manager conda --env-var PLATFORM=osx-64 --print > environment.devenv.osx-64.yml
+	conda lock --lockfile $(LOCKFILE) --platform osx-64 --file environment.devenv.osx-64.yml
 
 lock-win:
-	@$(CONDA_DEVENV) --name $(NAME) --file $(DEVENV) --env-manager $(CONDA) --env-var PLATFORM=win-64 --print > environment.devenv.win-64.yml
-	@$(CONDA_LOCK) $(CONDA_LOCK_OPTS) --lockfile $(LOCKFILE) --platform win-64 --file environment.devenv.win-64.yml
+	conda devenv --name $(NAME) --file $(DEVENV) --env-manager conda --env-var PLATFORM=win-64 --print > environment.devenv.win-64.yml
+	conda lock --lockfile $(LOCKFILE) --platform win-64 --file environment.devenv.win-64.yml
 
 render:
-	@$(CONDA_LOCK) render $(LOCKFILE) --kind env --filename-template environment.{platform}
-	@$(CONDA_LOCK) render $(LOCKFILE) --kind explicit --filename-template environment.{platform}.lock
+	conda lock render $(LOCKFILE) --kind env --filename-template environment.{platform}
+	conda lock render $(LOCKFILE) --kind explicit --filename-template environment.{platform}.lock
 	@if ! grep -e 'pytorch.*cuda' environment.linux-64.lock > /dev/null 2> /dev/null; then \
 		echo "Expected PyTorch with CUDA support for PLATFORM=linux-64. Check conda configuration."; \
 	fi
@@ -88,10 +81,10 @@ render:
 env: create-env install
 
 create-env:
-	@$(CONDA) $(CONDA_OPTS) create --name $(NAME) --file environment.$(PLATFORM).lock
+	conda create --name $(NAME) --file environment.$(PLATFORM).lock
 
 update-env:
-	@$(CONDA) $(CONDA_OPTS) update --name $(NAME) --file environment.$(PLATFORM).lock --prune
+	conda update --name $(NAME) --file environment.$(PLATFORM).lock --prune
 
 install:
-	@$(CONDA) $(CONDA_OPTS) run --name $(NAME) pip install $(PIP_INSTALL_OPTS) ./$(ROOT)[utils]
+	conda run --name $(NAME) pip install $(PIP_INSTALL_OPTS) ./$(ROOT)[utils]
diff --git a/conda/README.md b/conda/README.md
@@ -5,7 +5,7 @@ Conda environment configurations for `deepali` libraries.
 
 ## Create environment
 
-If not done before, install either [Miniconda](https://docs.conda.io/en/latest/miniconda.html) or [Anaconda](https://www.anaconda.com/).
+If not done before, install either [Anaconda], [Miniconda], or [Mambaforge].
 
 A conda environment for this project can be created using the `env` Makefile target, i.e.,
 
@@ -22,7 +22,7 @@ NAME=deepali
 PLATFORM=linux-64
 
 conda create --name $NAME --file environment.$PLATFORM.lock
-conda run --name $NAME pip install [--editable] ..
+conda run --name $NAME pip install ..[utils]
 ```
 
 where `PLATFORM` is one of the following values.
@@ -38,16 +38,21 @@ where `PLATFORM` is one of the following values.
 
 The following tools are required to update the generated dependency files.
 
-1. Install [Miniconda](https://docs.conda.io/en/latest/miniconda.html): Package dependency management tool.
-2. Install [mamba](https://mamba.readthedocs.io/en/latest/): Faster dependency resolution and more informative error messages.
-   - `conda install mamba=0.23 --name base --channel conda-forge`
-3. Install [conda-devenv](https://conda-devenv.readthedocs.io/en/latest/): Advanced conda environment configuration such as conditional dependencies.
-   - `conda install conda-devenv=2.3 --name base --channel conda-forge`
-4. Install [conda-lock](https://conda-incubator.github.io/conda-lock/): Lock versions of dependencies and generate explicit lockfiles.
-   - `conda install conda-lock=1.0 --name base --channel conda-forge`
+1. Install [Mambaforge]: Package dependency management tool.
+3. Install [conda-devenv]: Advanced conda environment configuration such as conditional dependencies.
+   - `mamba --no-banner install conda-devenv=2.3 --name base --channel conda-forge`
+4. Install [conda-lock]: Lock versions of dependencies and generate explicit lockfiles.
+   - `mamba --no-banner install conda-lock=1.0 --name base --channel conda-forge`
 
 After editing the `environment.devenv.yml` file to add, remove, or update required and optional dependencies, run the following command to re-generate the `environment.conda-lock.yml` and `environment.*.lock` files.
 
 ```
 make all
 ```
+
+
+[Anaconda]: https://www.anaconda.com/
+[Mambaforge]: https://mamba.readthedocs.io/en/latest/installation.html
+[Miniconda]: https://docs.conda.io/en/latest/miniconda.html
+[conda-devenv]: https://conda-devenv.readthedocs.io/en/latest/
+[conda-lock]: https://conda-incubator.github.io/conda-lock/