simplify build container (#346)

* try and see if this works?

* ok let's try

* Update sc-dandelion_test.def

* ok

* don't need to compile singularity anymore

* come on stop failing!

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* need to fix conda

* try

* Update sc-dandelion_test.def

* ist it something like this

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* does this help?

* oops

* Update sc-dandelion_test.def

* can i init?

* Update setup_mamba.sh

* Update prepare_database.py

* Update prepare_database.py

* Update prepare_database.py

* Update setup_mamba.sh

* hmm

* Update setup_mamba.sh

* Update setup_mamba.sh

* Update environment_test.yml

* Update prepare_database.py

* try and fix the input?

* Update prepare_database.py

* Update prepare_database.py

* Update prepare_database.py

* test this

* oops forgot about this

* Update prepare_ogrdb_database.py

* does this use db correctly?

* Update _preprocessing.py

* vscode

* Update prepare_ogrdb_database.py

* Update prepare_ogrdb_database.py

* Update prepare_ogrdb_database.py

* Update prepare_ogrdb_database.py

* Update prepare_ogrdb_database.py

* add ogrdb aux

* add files

* Update prepare_ogrdb_database.py

* update database

* move optional_file folder

* Update prepare_ogrdb_database.py

* update container definitions

* add more places that can accept db and strain

* Update test_mouse_ogrdb.py

* oops

* fix tests for now.

* black and add more info

* Update prepare_ogrdb_database.py

* add new merged fasta files

* update the argument

* Update _preprocessing.py

* seems like ogrdb is only compatible in strict mode

* download some files required from igblast

* ok this should fix it.

* remove unnecessary database files

* Update prepare_imgt_database.py

* Update _preprocessing.py

* reduce repetition

* Update tests.yml

* try and see if this works?

* ok let's try

* Update sc-dandelion_test.def

* ok

* don't need to compile singularity anymore

* come on stop failing!

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* need to fix conda

* try

* Update sc-dandelion_test.def

* ist it something like this

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* Update sc-dandelion_test.def

* does this help?

* oops

* Update sc-dandelion_test.def

* can i init?

* Update setup_mamba.sh

* Update prepare_database.py

* Update prepare_database.py

* Update prepare_database.py

* Update setup_mamba.sh

* hmm

* Update setup_mamba.sh

* Update setup_mamba.sh

* Update environment_test.yml

* Update prepare_database.py

* try and fix the input?

* Update prepare_database.py

* Update prepare_database.py

* Update prepare_database.py

* test this

* oops forgot about this

* Update prepare_ogrdb_database.py

* does this use db correctly?

* Update _preprocessing.py

* vscode

* Update prepare_ogrdb_database.py

* Update prepare_ogrdb_database.py

* Update prepare_ogrdb_database.py

* Update prepare_ogrdb_database.py

* Update prepare_ogrdb_database.py

* add ogrdb aux

* add files

* Update prepare_ogrdb_database.py

* update database

* move optional_file folder

* Update prepare_ogrdb_database.py

* update container definitions

* add more places that can accept db and strain

* Update test_mouse_ogrdb.py

* oops

* fix tests for now.

* black and add more info

* Update prepare_ogrdb_database.py

* add new merged fasta files

* update the argument

* Update _preprocessing.py

* seems like ogrdb is only compatible in strict mode

* download some files required from igblast

* ok this should fix it.

* remove unnecessary database files

* Update prepare_imgt_database.py

* Update _preprocessing.py

* reduce repetition

.github/workflows/publish_pypi.yml

@@ -12,11 +12,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - name: Set up checkout action
+        uses: actions/checkout@v3
       - name: Set up Python
         uses: actions/setup-python@v3
-        with:
-          python-version: "3.7"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.github/workflows/singularity_container-install.yml

@@ -41,54 +41,18 @@ jobs:
     if: needs.changes.outputs.keepgoing == 'true'
     runs-on: ubuntu-latest
     steps:
-      - name: Set up Go 1.13
-        uses: actions/setup-go@v1
-        with:
-          go-version: 1.13
-        id: go
-
-      - name: Install Dependencies
-        run: |
-          sudo apt-get update && sudo apt-get install -y \
-            build-essential \
-            libssl-dev \
-            uuid-dev \
-            libgpgme11-dev \
-            squashfs-tools \
-            libseccomp-dev \
-            pkg-config
-      - name: Install Singularity
-        env:
-          SINGULARITY_VERSION: 3.8.1
-          GOPATH: /tmp/go
-        run: |
-          mkdir -p $GOPATH
-          sudo mkdir -p /usr/local/var/singularity/mnt && \
-          mkdir -p $GOPATH/src/github.com/sylabs && \
-          cd $GOPATH/src/github.com/sylabs && \
-          wget -qO- https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz | \
-          tar xzv && \
-          cd singularity-ce-${SINGULARITY_VERSION} && \
-          ./mconfig -p /usr/local && \
-          make -C builddir && \
-          sudo make -C builddir install
       - name: Check out code for the container build
-        uses: actions/checkout@v2
-
+        uses: actions/checkout@v3
+      - name: Setup Singularity
+        uses: singularityhub/install-singularity@main
       - name: Extract repository location
         shell: bash
         run: |
-          echo "location=$(echo "  - git+https://www.github.com/${GITHUB_REPOSITORY}@${GITHUB_REF#refs/heads/}")" >> $GITHUB_OUTPUT
+          echo "location=$(echo "      - git+https://www.github.com/${GITHUB_REPOSITORY}@${GITHUB_REF#refs/heads/}")" >> $GITHUB_OUTPUT
         id: extract_location
-
       - name: Build Container
         run: |
-          ls container
           cd container
-          wget https://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.19.0/ncbi-igblast-1.19.0-x64-linux.tar.gz
-          wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-x64-linux.tar.gz
-          tar -xzvf ncbi-igblast-1.19.0-x64-linux.tar.gz
-          tar -xzvf ncbi-blast-2.13.0+-x64-linux.tar.gz
           echo '${{ steps.extract_location.outputs.location }}' >> environment_test.yml
           sudo -E singularity build --notest sc-dandelion.sif sc-dandelion_test.def
       - name: Test Container

.github/workflows/singularity_container-install_weekly.yml

@@ -8,54 +8,18 @@ jobs:
   container:
     runs-on: ubuntu-latest
     steps:
-      - name: Set up Go 1.13
-        uses: actions/setup-go@v1
-        with:
-          go-version: 1.13
-        id: go
-
-      - name: Install Dependencies
-        run: |
-          sudo apt-get update && sudo apt-get install -y \
-            build-essential \
-            libssl-dev \
-            uuid-dev \
-            libgpgme11-dev \
-            squashfs-tools \
-            libseccomp-dev \
-            pkg-config
-      - name: Install Singularity
-        env:
-          SINGULARITY_VERSION: 3.8.1
-          GOPATH: /tmp/go
-        run: |
-          mkdir -p $GOPATH
-          sudo mkdir -p /usr/local/var/singularity/mnt && \
-          mkdir -p $GOPATH/src/github.com/sylabs && \
-          cd $GOPATH/src/github.com/sylabs && \
-          wget -qO- https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz | \
-          tar xzv && \
-          cd singularity-ce-${SINGULARITY_VERSION} && \
-          ./mconfig -p /usr/local && \
-          make -C builddir && \
-          sudo make -C builddir install
       - name: Check out code for the container build
-        uses: actions/checkout@v2
-
+        uses: actions/checkout@v3
+      - name: Setup Singularity
+        uses: singularityhub/install-singularity@main
       - name: Extract repository location
         shell: bash
         run: |
-          echo "location=$(echo "  - git+https://www.github.com/${GITHUB_REPOSITORY}@${GITHUB_REF#refs/heads/}")" >> $GITHUB_OUTPUT
+          echo "location=$(echo "      - git+https://www.github.com/${GITHUB_REPOSITORY}@${GITHUB_REF#refs/heads/}")" >> $GITHUB_OUTPUT
         id: extract_location
-
       - name: Build Container
         run: |
-          ls container
           cd container
-          wget https://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.19.0/ncbi-igblast-1.19.0-x64-linux.tar.gz
-          wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-x64-linux.tar.gz
-          tar -xzvf ncbi-igblast-1.19.0-x64-linux.tar.gz
-          tar -xzvf ncbi-blast-2.13.0+-x64-linux.tar.gz
           echo '${{ steps.extract_location.outputs.location }}' >> environment_test.yml
           sudo -E singularity build --notest sc-dandelion.sif sc-dandelion_test.def
       - name: Test Container

.github/workflows/tests.yml

@@ -202,7 +202,7 @@ jobs:
           coverage report
 
       - name: Upload coverage to Codecov
-        if: matrix.config.os == 'ubuntu-latest' && matrix.config.python-version == '3.10' &&  github.actor != 'dependabot[bot]'
+        if: matrix.config.os == 'ubuntu-latest' && matrix.config.python-version == '3.10' &&  github.actor != 'dependabot[bot]' &&  github.actor != 'zktuong'
         uses: codecov/codecov-action@v1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}