Fix repo name

CHANGELOG.md

@@ -1,5 +1,7 @@
 ## Tools development version
 
+- Fix bug in `ccbr_tools install` where CCBR/Tools & CCBR/actions were using incorrect repo names. (#53, @kelly-sovacool)
+
 ## Tools 0.3.0
 
 - Allow relaxed version with only major and minor components in `match_semver()` with `strict_semver=False`. (#49, @kelly-sovacool)

src/ccbr_tools/pipeline/hpc.py

@@ -70,7 +70,7 @@ class Biowulf(Cluster):
     GROUP = "CCBR_Pipeliner"
     PIPELINES_HOME = pathlib.Path("/data/CCBR_Pipeliner/Pipelines")
     TOOLS_HOME = pathlib.Path("/data/CCBR_Pipeliner/Tools")
-    CONDA_ACTIVATE = '. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh && conda activate py311'
+    CONDA_ACTIVATE = '. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate py311'
 
     def __init__(self):
         super().__init__()
@@ -101,7 +101,7 @@ class FRCE(Cluster):
     GROUP = "nci-frederick-ccbr-pipelines"
     PIPELINES_HOME = pathlib.Path("/mnt/projects/CCBR-Pipelines/pipelines")
     TOOLS_HOME = pathlib.Path("/mnt/projects/CCBR-Pipelines/tools")
-    CONDA_ACTIVATE = '. "/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh && conda activate py311'
+    CONDA_ACTIVATE = '. "/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh" && conda activate py311'
 
     def __init__(self):
         super().__init__()

src/ccbr_tools/software.py

@@ -23,6 +23,9 @@
             self.version_re
         ), f"Invalid version format '{version}' - Must be a valid semantic version."
 
+    def __repr__(self):
+        return f"{self.__class__.__name__}({self.name}, {self.version})"
+
     def path(self, hpc: Cluster, branch_tag=None):
         hidden_dir = self.hidden_version if not branch_tag else f".{branch_tag}"
         return hpc.TOOLS_HOME / self.name / hidden_dir
@@ -70,10 +73,15 @@
 class PythonTool(Software):
     def __init__(self, name, version):
         super(PythonTool, self).__init__(name, version)
+        self.repo_name = name.replace("ccbr_", "")
 
     def install(self, hpc: Cluster, branch_tag=None):
         return Installer.python(self, hpc, branch_tag=branch_tag)
 
+    @property
+    def url(self):
+        return f"https://github.com/CCBR/{self.repo_name}.git"
+
 
 class BashTool(Software):
     def __init__(self, name, version):
@@ -128,10 +136,10 @@
 SET_SYMLINK = """rm -if {MAJOR_MINOR_VERSION}
 ln -s {PATH} {MAJOR_MINOR_VERSION}"""
 
-INSTALL_SCRIPT = """newgrp {GROUP}
-{CONDA_ACTIVATE}
+INSTALL_SCRIPT = """{CONDA_ACTIVATE}
 {INSTALL}
-chmod -R a+rX {PATH}"""
+chmod -R a+rX {PATH}
+chown -R :{GROUP} {PATH}"""
 
 
 def install(
@@ -148,7 +156,7 @@
     script = install_script.format(
         GROUP=hpc.GROUP,
         CONDA_ACTIVATE=hpc.CONDA_ACTIVATE,
-        INSTALL=tool.install(hpc),
+        INSTALL=tool.install(hpc, branch_tag=branch_tag),
         PATH=tool.path(hpc),
     )
     if not tool.is_dev_version:
@@ -159,4 +167,4 @@
     if dryrun:
         print(script)
     else:
-        shell_run(script, shell=True, check=True, capture_output=False)
+        shell_run(script, shell=True, capture_output=False)

tests/test_pipeline_hpc.py

@@ -13,6 +13,8 @@ def test_hpc_biowulf():
             hpc.__repr__().startswith(
                 "<class 'ccbr_tools.pipeline.hpc.Biowulf'>({'name': 'biowulf'"
             ),
+            hpc.CONDA_ACTIVATE
+            == '. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate py311',
         ]
     )
 
@@ -25,6 +27,8 @@ def test_hpc_frce():
             hpc.name == "frce",
             "/mnt/projects/CCBR-Pipelines/bin" in hpc.env_vars,
             hpc.singularity_sif_dir == "/mnt/projects/CCBR-Pipelines/SIFs",
+            hpc.CONDA_ACTIVATE
+            == '. "/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh" && conda activate py311',
         ]
     )
 

tests/test_software.py

@@ -0,0 +1,35 @@
+from ccbr_tools.software import Software
+from ccbr_tools.pipeline.hpc import Biowulf
+
+
+def test_python():
+    assert all(
+        [
+            Software.create_software("ccbr_tools", "v0.3.2").url
+            == "https://github.com/CCBR/tools.git",
+            Software.create_software("ccbr_actions", "v0.1.2").url
+            == "https://github.com/CCBR/actions.git",
+            Software.create_software("ccbr_actions", "v1.0.0-dev").install(
+                hpc=Biowulf, branch_tag="main"
+            )
+            == "pip install git+https://github.com/CCBR/actions.git@main -t /data/CCBR_Pipeliner/Tools/ccbr_actions/.v1.0.0-dev",
+        ]
+    )
+
+
+def test_pipelines():
+    assert all(
+        [
+            Software.create_software("CHAMPAGNE", "v0.3.0").install(hpc=Biowulf)
+            == "pip install git+https://github.com/CCBR/[email protected] -t /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0",
+            Software.create_software("XAVIER", "v3.0.1").install(hpc=Biowulf)
+            == "git clone --depth 1 --single-branch --branch v3.0.1 https://github.com/CCBR/XAVIER.git /data/CCBR_Pipeliner/Pipelines/XAVIER/.v3.0.1",
+        ]
+    )
+
+
+def test_bash():
+    assert (
+        Software.create_software("permfix", "v1.2.3").install(Biowulf)
+        == "git clone --depth 1 --single-branch --branch v1.2.3 https://github.com/CCBR/permfix.git /data/CCBR_Pipeliner/Tools/permfix/.v1.2.3"
+    )