redo to close #187 and to close #188 (#195)

* redo to close #187 and to close #188
Signed-off-by: vsoch <vsochat@stanford.edu>

CHANGELOG.md

@@ -17,6 +17,7 @@ The client here will eventually be released as "spython" (and eventually to
 singularity on pypi), and the versions here will coincide with these releases.
 
 ## [master](https://github.com/singularityhub/singularity-cli/tree/master)
+ - parser bugfixes, arg from Docker not properly parsed (0.2.1)
  - version checks removed to support Singularity 3.x and above (0.2.0)
  - adding support for SIF (oras pull) (0.1.18)
  - updating CI/tests and fixing deprecations (warnings) (0.1.17)

setup.py

@@ -104,7 +104,6 @@ def get_requirements(lookup=None):
             "Topic :: Software Development",
             "Topic :: Scientific/Engineering",
             "Operating System :: Unix",
-            "Programming Language :: Python :: 2.7",
             "Programming Language :: Python :: 3",
         ],
         entry_points={"console_scripts": ["spython=spython.client:main"]},

spython/main/parse/parsers/base.py

@@ -155,6 +155,6 @@ def _replace_from_dict(self, string, args):
         string: the string with replacements made
         """
         for key, value in args.items():
-            if re.search(r"\$(" + key + r"|\{[^}]*\})", string):
-                string = re.sub(r"\$(" + key + r"|\{[^}]*\})", value, string)
+            if re.search("([$]" + key + "|[$][{]" + key + "[}])", string):
+                string = re.sub("([$]" + key + "|[$]{" + key + "[}])", value, string)
         return string

spython/main/parse/writers/docker.py

@@ -71,16 +71,16 @@ def validate_stage(self, parser):
         if parser.fromHeader is None:
             bot.exit("Dockerfile requires a fromHeader.")
 
-            # Parse the provided name
-            uri_regexes = [_reduced_uri, _default_uri, _docker_uri]
+        # Parse the provided name
+        uri_regexes = [_reduced_uri, _default_uri, _docker_uri]
 
-            for r in uri_regexes:
-                match = r.match(parser.fromHeader)
-                if match:
-                    break
+        for r in uri_regexes:
+            match = r.match(parser.fromHeader)
+            if match:
+                break
 
-            if not match:
-                bot.exit("FROM header %s not valid." % parser.fromHeader)
+        if not match:
+            bot.exit("FROM header %s not valid." % parser.fromHeader)
 
     def convert(self, runscript="/bin/bash", force=False):
         """convert is called by the parent class to convert the recipe object

spython/tests/testdata/docker2singularity/argsub.def

@@ -0,0 +1,38 @@
+Bootstrap: docker
+From: nvidia/cuda:11.1.1-cudnn8-devel-ubuntu20.04
+Stage: spython-base
+
+%files
+./requirements.txt /workspace
+%labels
+maintainer="Dong Wang"
+%post
+CUDA_VERSION=11.1.1
+OS_VERSION=20.04
+
+
+
+
+PATH="/root/miniconda3/bin:${PATH}"
+PATH="/root/miniconda3/bin:${PATH}"
+DEBIAN_FRONTEND=noninteractive
+
+SHELL ["/bin/bash", "-c"]
+
+apt-get update && apt-get upgrade -y &&\
+apt-get install -y wget python3-pip
+
+python3 -m pip install --upgrade pip
+
+cd /workspace
+python3 -m pip install -r /workspace/requirements.txt and &&\
+rm /workspace/requirements.txt
+
+%environment
+export PATH="/root/miniconda3/bin:${PATH}"
+%runscript
+cd /workspace
+exec /bin/bash /bin/bash "$@"
+%startscript
+cd /workspace
+exec /bin/bash /bin/bash "$@"

spython/tests/testdata/docker2singularity/argsub.docker

@@ -0,0 +1,25 @@
+ARG CUDA_VERSION=11.1.1
+ARG OS_VERSION=20.04
+
+FROM nvidia/cuda:${CUDA_VERSION}-cudnn8-devel-ubuntu${OS_VERSION}
+
+LABEL maintainer="Dong Wang"
+
+
+ENV PATH="/root/miniconda3/bin:${PATH}"
+ARG PATH="/root/miniconda3/bin:${PATH}"
+ARG DEBIAN_FRONTEND=noninteractive
+
+SHELL ["/bin/bash", "-c"]
+
+RUN apt-get update && apt-get upgrade -y &&\
+apt-get install -y wget python3-pip
+
+RUN python3 -m pip install --upgrade pip
+
+WORKDIR /workspace
+ADD ./requirements.txt /workspace
+RUN python3 -m pip install -r /workspace/requirements.txt and &&\
+rm /workspace/requirements.txt
+
+CMD ["/bin/bash"]

spython/version.py

@@ -5,7 +5,7 @@
 # with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
 
 
-__version__ = "0.2.0"
+__version__ = "0.2.1"
 AUTHOR = "Vanessa Sochat"
 AUTHOR_EMAIL = "vsoch@users.noreply.github.com"
 NAME = "spython"