Hotfix: release/7.1.1 (setup.py and package_data) (#586)

* update setup * buncha inits * move req to setup * remove requirements * remove req.txt * changelog * update docs
Clinical-Genomics · Mar 4, 2021 · 73c4a1d · 73c4a1d
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diff --git a/.github/workflows/pytest_and_coveralls.yml b/.github/workflows/pytest_and_coveralls.yml
@@ -38,8 +38,8 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate balsamic
-          pip install --no-cache-dir -r requirements-dev.txt -r requirements.txt
-          pip install -e .
+          pip install --no-cache-dir -r requirements-dev.txt
+          pip install .
 
       # Run PyTest
       - name: Run PyTest

diff --git a/BALSAMIC/assets/MVL/MSK_IMPAKT_supp_S11_Cheng_2015.bed.gz b/BALSAMIC/assets/MVL/MSK_IMPAKT_supp_S11_Cheng_2015.bed.gz
diff --git a/BALSAMIC/assets/MVL/MSK_IMPAKT_supp_S11_Cheng_2015.bed.gz.tbi b/BALSAMIC/assets/MVL/MSK_IMPAKT_supp_S11_Cheng_2015.bed.gz.tbi
diff --git a/BALSAMIC/assets/MVL/MSK_IMPAKT_supp_S11_Cheng_2015.tsv b/BALSAMIC/assets/MVL/MSK_IMPAKT_supp_S11_Cheng_2015.tsv
diff --git a/BALSAMIC/assets/internal_reference/hg19/README.md b/BALSAMIC/assets/internal_reference/hg19/README.md
diff --git a/BALSAMIC/assets/internal_reference/hg19/ncbiRefSeq.txt b/BALSAMIC/assets/internal_reference/hg19/ncbiRefSeq.txt
diff --git a/BALSAMIC/assets/internal_reference/hg19/ncbiRefSeqPsl.txt b/BALSAMIC/assets/internal_reference/hg19/ncbiRefSeqPsl.txt
diff --git a/BALSAMIC/assets/internal_reference/hg19/seqNcbiRefSeq.txt b/BALSAMIC/assets/internal_reference/hg19/seqNcbiRefSeq.txt
diff --git a/BALSAMIC/assets/picard-2.18.11-3-gc6e797f-SNAPSHOT-all.jar b/BALSAMIC/assets/picard-2.18.11-3-gc6e797f-SNAPSHOT-all.jar
diff --git a/BALSAMIC/assets/picard-2.18.5-4-g63d860e-SNAPSHOT-all.jar b/BALSAMIC/assets/picard-2.18.5-4-g63d860e-SNAPSHOT-all.jar
diff --git a/BALSAMIC/assets/picard-2.23.2-201-g922891d-SNAPSHOT-all.jar b/BALSAMIC/assets/picard-2.23.2-201-g922891d-SNAPSHOT-all.jar
diff --git a/BALSAMIC/assets/report_template/__init__.py b/BALSAMIC/assets/report_template/__init__.py
diff --git a/BALSAMIC/assets/scripts/__init__.py b/BALSAMIC/assets/scripts/__init__.py
diff --git a/BALSAMIC/assets/sentieon_models/__init__.py b/BALSAMIC/assets/sentieon_models/__init__.py
diff --git a/BALSAMIC/assets/stargazer_5.2.2.tar.gz b/BALSAMIC/assets/stargazer_5.2.2.tar.gz
diff --git a/BALSAMIC/assets/vcfanno/__init__.py b/BALSAMIC/assets/vcfanno/__init__.py
diff --git a/BALSAMIC/config/__init__.py b/BALSAMIC/config/__init__.py
diff --git a/BALSAMIC/containers/__init__.py b/BALSAMIC/containers/__init__.py
diff --git a/BALSAMIC/containers/align_qc/__init__.py b/BALSAMIC/containers/align_qc/__init__.py
diff --git a/BALSAMIC/containers/annotate/__init__.py b/BALSAMIC/containers/annotate/__init__.py
diff --git a/BALSAMIC/containers/coverage_qc/__init__.py b/BALSAMIC/containers/coverage_qc/__init__.py
diff --git a/BALSAMIC/containers/varcall_cnvkit/__init__.py b/BALSAMIC/containers/varcall_cnvkit/__init__.py
diff --git a/BALSAMIC/containers/varcall_py27/__init__.py b/BALSAMIC/containers/varcall_py27/__init__.py
diff --git a/BALSAMIC/containers/varcall_py36/__init__.py b/BALSAMIC/containers/varcall_py36/__init__.py
diff --git a/BALSAMIC/dev_report/__init__.py b/BALSAMIC/dev_report/__init__.py
diff --git a/BALSAMIC/snakemake_rules/__init__.py b/BALSAMIC/snakemake_rules/__init__.py
diff --git a/BALSAMIC/snakemake_rules/align/__init__.py b/BALSAMIC/snakemake_rules/align/__init__.py
diff --git a/BALSAMIC/snakemake_rules/annotation/__init__.py b/BALSAMIC/snakemake_rules/annotation/__init__.py
diff --git a/BALSAMIC/snakemake_rules/dragen_suite/__init__.py b/BALSAMIC/snakemake_rules/dragen_suite/__init__.py
diff --git a/BALSAMIC/snakemake_rules/quality_control/__init__.py b/BALSAMIC/snakemake_rules/quality_control/__init__.py
diff --git a/BALSAMIC/snakemake_rules/umi/__init__.py b/BALSAMIC/snakemake_rules/umi/__init__.py
diff --git a/BALSAMIC/snakemake_rules/variant_calling/__init__.py b/BALSAMIC/snakemake_rules/variant_calling/__init__.py
diff --git a/BALSAMIC/workflows/__init__.py b/BALSAMIC/workflows/__init__.py
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,3 +1,12 @@
+[7.1.1]
+-------
+
+Fixed:
+^^^^^
+
+* Moved all requirements to setup.py, and added all package_data there. Clean up unused files.
+
+
 [7.1.0]
 -------
 

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -2,19 +2,4 @@
 include CHANGELOG.rst
 include LICENSE
 include README.rst
-include requirements.txt
 include requirements-dev.txt
-
-# config data
-recursive-include BALSAMIC/config *
-
-# assests
-recursive-include BALSAMIC/assets/scripts *
-recursive-include BALSAMIC/assets/sentieon_models *
-recursive-include BALSAMIC/assets/report_template *
-include BALSAMIC/assets/scout_config_template.yaml
-recursive-include BALSAMIC/assets/vcfanno *
-
-# SnakeMake assets
-recursive-include BALSAMIC/snakemake_rules *
-recursive-include BALSAMIC/workflows *
diff --git a/docs/install.rst b/docs/install.rst
@@ -17,11 +17,11 @@ Software Requirments
 Step 1. Installing BALSAMIC
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-1. Create a conda environment using ``BALSAMIC/conda/balsamic.yaml``:
+1. Create a conda environment:
 
 ::
 
-    conda env create --file BALSAMIC/conda/balsamic.yaml --name balsamic
+    conda create -c conda-forge -c defaults --name S_BALSAMIC python==3.7 pip
 
 
 2. Activate environment: 
@@ -36,7 +36,14 @@ Step 1. Installing BALSAMIC
 
 ::
 
-  pip install -r requirements.txt -e .
+  pip install --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC
+
+
+Or if you have repository cloned and want it in editable mode:
+
+::
+
+  pip install -e .
 
 
 Step 2. generate BALSAMIC cache and pull containers

diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.py b/setup.py
@@ -3,12 +3,6 @@
 
 here = os.path.abspath(os.path.dirname(__file__))
 
-try:
-    with open("requirements.txt", "r") as f:
-        install_requires = [x.strip() for x in f.readlines()]
-except IOError:
-    install_requires = []
-
 # Load the package's __version__.py module as a dictionary.
 about = {}
 with open(os.path.join(here, "BALSAMIC", "__version__.py")) as f:
@@ -20,11 +14,36 @@
     url="https://github.com/Clinical-Genomics/BALSAMIC",
     author="Hassan Foroughi Asl",
     author_email='[email protected]',
-    install_requires=install_requires,
+    install_requires=[
+        "click>=7.1.2",
+        "colorclass>=2.2.0",
+        "coloredlogs>=14.0",
+        "cyvcf2<0.10.0",
+        "graphviz>=0.14",
+        "gsutil==4.50",
+        "jinja2>=2.11.2",
+        "matplotlib>=3.3.0",
+        "networkx>=2.4",
+        "numpy>=1.19.2",
+        "pandas>1.1.0",
+        "psutil>=5.7.0",
+        "pydantic>=1.5.1",
+        "pygments>=2.6.1",
+        "pyyaml>=5.3.1",
+        "six>=1.12.0",
+        "snakemake==5.13.0",
+        "yapf>=0.30.0",
+        "h5py>=3.1.0",
+        "PyPDF2>=1.26.0",
+        "markdown==3.3.3",
+        "cryptography<3.4",
+    ],
     packages=find_packages(),
     package_data={
-        "assets": ["scripts/*R", "sentieon_models/*model", "vcfanno/*.toml"],
-        "config": ["*.json"]
+        "": [
+            "*.toml", "*.json", "*.R", "*.model", "*.yaml", "*.sh", "*.rule",
+            "*.smk", "*.awk", "*.html", "*.md"
+        ],
     },
     include_package_data=True,
     zip_safe=False,
-Original file line number
+Diff line change
@@ -1,3 +1,12 @@
+    [7.1.1]
+    -------
+    Fixed:
+    ^^^^^
+    * Moved all requirements to setup.py, and added all package_data there. Clean up unused files.
     [7.1.0]
     -------
@@ Expand Down @@