From f3a3f75c2199cd58bd8a4fb61e3063408f687349 Mon Sep 17 00:00:00 2001 From: Jason Hemann Date: Thu, 6 May 2021 10:30:41 -0400 Subject: [PATCH 1/2] Clarifying a few steps in the install MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit I ran across a few difficulties in installation and setup. Without these additions, I was seeing e.g. ``` Collecting rpy2 Downloading rpy2-3.4.4.tar.gz (187 kB) |████████████████████████████████| 187 kB 9.3 MB/s ERROR: Command errored out with exit status 1: command: /Users/jhemann/Documents/Trinity/tyrell/venv/bin/python3.9 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/lv/300nvm1d6lq_dmww4c8h9z680000gn/T/pip-install-jzjvdvx6/rpy2_8aca3d4c44d8453da3af9292c3e428ae/setup.py'"'"'; __file__='"'"'/private/var/folders/lv/300nvm1d6lq_dmww4c8h9z680000gn/T/pip-install-jzjvdvx6/rpy2_8aca3d4c44d8453da3af9292c3e428ae/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/lv/300nvm1d6lq_dmww4c8h9z680000gn/T/pip-pip-egg-info-y20nejf7 cwd: /private/var/folders/lv/300nvm1d6lq_dmww4c8h9z680000gn/T/pip-install-jzjvdvx6/rpy2_8aca3d4c44d8453da3af9292c3e428ae/ Complete output (4 lines): WARNING: The wheel package is not available. WARNING: The wheel package is not available. Error: rpy2 in API mode cannot be built without R in the PATH or R_HOME defined. Correct this or force ABI mode-only by defining the environment variable RPY2_CFFI_MODE=ABI ['cffi>=1.10.0', 'jinja2', 'pytz', 'tzlocal'] ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/cb/a5/354fdfc13ac30fd496c100a66587bbf7f0adcd320fa751311566f198bdbd/rpy2-3.4.4.tar.gz#sha256=e198862701bfc6d3da4a2fcf18910d71521b385283abdb2121e07b874add8e50 (from https://pypi.org/simple/rpy2/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ``` --- README.md | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 22c2ae7..ef64b84 100644 --- a/README.md +++ b/README.md @@ -7,15 +7,21 @@ Dev Environment Setup - It is preferable to have a dedicated virtualenv for this project: ``` $ git clone - $ cd Tyrell + $ cd + $ cd tyrell $ mkdir venv $ python3 -m venv venv $ source venv/bin/activate + $ cd .. ``` +- Install R if you have not. + - Make an editable install with `pip`. This would automatically handles package dependencies. One of our dependency, `z3-solver`, takes a long time to build. Please be patient. ``` + $ python3 -m pip install --upgrade pip + $ pip install wheel $ pip install -e ".[dev]" - $ python setup.py sdist # for package + $ python3 setup.py sdist # for package ``` - Test whether the installation is successful ``` From 6864491eaa90c0c6d90d9ba89a316bfa1db74a50 Mon Sep 17 00:00:00 2001 From: Jason Hemann Date: Wed, 5 Jan 2022 15:24:32 -0500 Subject: [PATCH 2/2] Adding additional steps for potentially missing packages --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index ef64b84..6bf8c7d 100644 --- a/README.md +++ b/README.md @@ -15,11 +15,11 @@ Dev Environment Setup $ cd .. ``` - Install R if you have not. - +- Install the R packages `dplyr`, `tidyr`, and `compare` - Make an editable install with `pip`. This would automatically handles package dependencies. One of our dependency, `z3-solver`, takes a long time to build. Please be patient. ``` $ python3 -m pip install --upgrade pip - $ pip install wheel + $ pip install wheel sexpdata rpy2 compare $ pip install -e ".[dev]" $ python3 setup.py sdist # for package ``` @@ -36,7 +36,7 @@ Dev Environment Setup $ python setup.py sdist ``` Tarball will be available at `dist/tyrell-.tar.gz` -- Build HTML documentations +- Build HTML documentation ``` $ cd docs $ make html