Fix Makefile

- remove cleaning build files, `pip install -e` should be used - `pip install -e` doesn't work with multiple files, use a for loop to install the submodules
ilastik · Sep 10, 2024 · a0d5695 · a0d5695
1 parent 5e75d22
commit a0d5695
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Showing 2 changed files with 22 additions and 32 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -2,7 +2,7 @@ version: 2
 jobs:
   checkout_code:
     docker:
-      - image: condaforge/mambaforge
+      - image: condaforge/miniforge3
     working_directory: ~/repo
     steps:
       - checkout
@@ -18,41 +18,37 @@ jobs:
       TIKTORCH_ENV_NAME: tiktorch-server-env
       TIKTORCH_ENV_PREFIX: /opt/conda/envs/tiktorch-server-env
     docker:
-      - image: condaforge/mambaforge
+      - image: condaforge/miniforge3
     working_directory: ~/repo
     steps:
       - restore_cache:
           keys:
             - v1-repo-{{ .Environment.CIRCLE_SHA1 }}
       - restore_cache:
           keys:
-            - v11-dependencies-{{ checksum "environment.yml" }}
-
+            - v11-dependencies-{{ .Environment.CIRCLE_SHA1 }}
       - run: conda config --set channel_priority strict
-      - run: mamba update -n base -c conda-forge --update-all
-      - run: mamba install -c conda-forge conda-build make boa
+      - run: conda update -n base -c conda-forge --update-all
+      - run: conda install -c conda-forge conda-build make boa
       - run: |
-          if [ ! -d ${TIKTORCH_ENV_PREFIX} ]; then
               echo "Creating new environment ${TIKTORCH_ENV_NAME}"
               make devenv
-          fi
-
       - save_cache:
           paths:
             - /opt/conda/envs
-          key: v11-dependencies-{{ checksum "environment.yml" }}
+          key: v11-dependencies-{{ .Environment.CIRCLE_SHA1 }}
 
   pre_commit_check:
     docker:
-      - image: condaforge/mambaforge
+      - image: condaforge/miniforge3
     working_directory: ~/repo
     steps:
       - restore_cache:
           keys:
             - v1-repo-{{ .Environment.CIRCLE_SHA1 }}
       - restore_cache:
           keys:
-            - v11-dependencies-{{ checksum "environment.yml" }}
+            - v11-dependencies-{{ .Environment.CIRCLE_SHA1 }}
 
       - run:
           name: run pre-commit
@@ -63,15 +59,15 @@ jobs:
 
   tests:
     docker:
-      - image: condaforge/mambaforge
+      - image: condaforge/miniforge3
     working_directory: ~/repo
     steps:
       - restore_cache:
           keys:
             - v1-repo-{{ .Environment.CIRCLE_SHA1 }}
       - restore_cache:
           keys:
-            - v11-dependencies-{{ checksum "environment.yml" }}
+            - v11-dependencies-{{ .Environment.CIRCLE_SHA1 }}
 
       - run:
           name: run tests
@@ -83,15 +79,15 @@ jobs:
 
   build_conda_packages:
     docker:
-      - image: condaforge/mambaforge
+      - image: condaforge/miniforge3
     working_directory: ~/repo
     steps:
       - restore_cache:
           keys:
             - v1-repo-{{ .Environment.CIRCLE_SHA1 }}
 
-      - run: mamba config --set channel_priority strict
-      - run: mamba install -c conda-forge conda-build anaconda-client boa
+      - run: conda config --set channel_priority strict
+      - run: conda install -c conda-forge conda-build anaconda-client boa
       - run:
           name: build packages
           command: |

diff --git a/Makefile b/Makefile
@@ -1,18 +1,7 @@
 SHELL=/bin/bash
 ROOT_DIR:=$(shell dirname $(realpath $(firstword $(MAKEFILE_LIST))))
 TIKTORCH_ENV_NAME ?= tiktorch-server-env
-
-sample_model:
-	cd tests/data/dummy && zip -r $(ROOT_DIR)/dummy.tmodel ./*
-
-unet2d:
-	cd tests/data/unet2d && zip -r $(ROOT_DIR)/unet2d.tmodel ./*
-
-unet2d_onnx:
-	cd tests/data/unet2d_onnx && zip -r $(ROOT_DIR)/onnx.tmodel ./*
-
-dummy_tf:
-	cd tests/data/dummy_tensorflow && zip -r $(ROOT_DIR)/dummy_tf.tmodel ./*
+SUBMODULES = ./vendor/core-bioimage-io-python ./vendor/spec-bioimage-io
 
 protos:
 	python -m grpc_tools.protoc -I./proto --python_out=tiktorch/proto/ --grpc_python_out=tiktorch/proto/ ./proto/*.proto
@@ -21,18 +10,23 @@ protos:
 version:
 	python -c "import sys; print(sys.version)"
 
-
 devenv:
 	. $$(conda info --base)/etc/profile.d/conda.sh
 	mamba env create --file environment.yml --name $(TIKTORCH_ENV_NAME)
-	conda run -n $(TIKTORCH_ENV_NAME) pip install . ./vendor/core-bioimage-io-python ./vendor/spec-bioimage-io
+	make install_submodules
 
 run_server:
 	. $$(conda info --base)/etc/profile.d/conda.sh; conda activate $(TIKTORCH_ENV_NAME); python -m tiktorch.server
 
+install_submodules:
+	@echo "Installing submodules $(SUBMODULES)"
+	@for package in $(SUBMODULES) ; do \
+		echo $$package ; \
+		conda run -n $(TIKTORCH_ENV_NAME) pip install -e $$package ; \
+	done
 
 remove_devenv:
 	conda env remove --yes --name $(TIKTORCH_ENV_NAME)
 
 
-.PHONY: protos version sample_model devenv remove_devenv dummy_tf
+.PHONY: *