def run_module(root, module, build_script='make.py', osname=None):
""".. Run module.
Runs script `build_script` in module directory `module` relative to root of repository `root`.
Parameters
----------
root : str
Directory of root.
module: str
Name of module.
build_script : str
Name of build script. Defaults to ``make.py``.
osname : str, optional
Name of OS. Used to determine syntax of system command. Defaults to ``os.name``.
Returns
-------
None
Example
-------
The following code runs the script ``root/module/make.py``.
.. code-block:: python
run_module(root = 'root', module = 'module')
"""
osname = osname if osname else os.name # https://github.com/sphinx-doc/sphinx/issues/759
try:
module_dir = os.path.join(root, module)
os.chdir(module_dir)
build_script = norm_path(build_script)
if not os.path.isfile(build_script):
raise CritError(messages.crit_error_no_file % build_script)
message = 'Running module `%s`' % module
message = format_message(message)
message = colored(message, attrs=['bold'])
print('\n' + message)
status = os.system(
'%s %s' %
(metadata.default_executables[osname]['python'], build_script))
if status != 0:
raise ProgramError()
except ProgramError:
sys.exit()
except:
error_message = 'Error with `run_module`. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def zip_dir(source_dir, zip_dest):
""".. Zip directory to file.
Zips directory ``source_dir`` to file ``zip_dest``.
Parameters
----------
source_dir : str
Path of directory to zip.
zip_dest : str
Destination of zip file.
Returns
-------
None
"""
try:
with zipfile.ZipFile('%s' % (zip_dest), 'w', zipfile.ZIP_DEFLATED, allowZip64 = True) as z:
source_dir = norm_path(source_dir)
for root, dirs, files in os.walk(source_dir):
for f in files:
file_path = os.path.join(root, f)
file_name = os.path.basename(file_path)
z.write(file_path, file_name)
message = 'Zipped: `%s` as `%s`' % (file_path, file_name)
print(colored(message, metadata.color_success))
except:
error_message = 'Error with `zip_dir`. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def get_modified_sources(paths, source_map, depth=float('inf')):
""".. Get source files considered changed by git.
Checks the modification status for all sources contained in list ``source_map`` (returned by `sourcing functions`_). Produces warning if sources have been modified according to git. When walking through sources, float ``depth`` determines level of depth to walk. Warning messages are appended to file ``makelog``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
source_map : list
Mapping of sources (returned from `sourcing functions`_).
depth : float, optional
Level of depth when walking through source directories. Defaults to infinite.
Path Keys
---------
makelog : str
Path of makelog.
Returns
-------
overlap : list
List of source files considered changed by git.
Notes
-----
"""
try:
source_list = [source for source, destination in source_map]
source_list = [glob_recursive(source, depth) for source in source_list]
source_files = [f for source in source_list for f in source]
source_files = set(source_files)
try:
repo = git.Repo('.', search_parent_directories=True)
except:
raise_from(CritError(messages.crit_error_no_repo), None)
modified = _get_git_status(repo)
overlap = [l for l in source_files if l in modified]
if overlap:
if len(overlap) > 100:
overlap = overlap[0:100]
overlap = overlap + [
"and more (file list truncated due to length)"
]
message = messages.warning_modified_files % '\n'.join(overlap)
write_to_makelog(paths, message)
print(colored(message, metadata.color_failure))
except:
error_message = 'Error with `get_modified_sources`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def _check_stata_output(output):
""".. Check Stata output"""
regex = "end of do-file[\s]*r\([0-9]*\);"
if re.search(regex, output):
error_message = 'Stata program executed with errors.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, 'See makelog for more detail.'),
None)
def clear_dir(dir_list):
""".. Clear directory. Create directory if nonexistent.
Clears all directories in list ``dir_list`` using system command.
Safely clears symbolic links. Directories can be specified with the * shell pattern
(see `here <https://www.gnu.org/software/findutils/manual/html_node/find_html/Shell-Pattern-Matching.html>`__).
Note
----
To clear a directory means to remove all contents of a directory.
If the directory is nonexistent, the directory is created,
unless the directory is specified via shell pattern.
Parameters
----------
dir_list : str, list
Directory or list of directories to clear.
Returns
-------
None
Example
-------
The following code clears directories ``dir1`` and ``dir2``.
.. code-block:: python
clear_dir(['dir1', 'dir2'])
The following code clears directories beginning with ``dir``.
.. code-block:: python
clear_dir(['dir*'])
"""
try:
dir_list = convert_to_list(dir_list, 'dir')
dir_glob = []
for dir_path in dir_list:
expand = glob.glob(dir_path)
expand = expand if expand else [dir_path]
dir_glob.extend(expand)
remove_dir(dir_glob, quiet = True)
for dir_path in dir_glob:
os.makedirs(dir_path)
message = 'Cleared: `%s`' % dir_path
print(colored(message, metadata.color_success))
except:
error_message = 'Error with `clear_dir`. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def check_conda_status(root):
""".. Makes sure that the repository is being run with conda and is up to date.
Checks that conda is activated.
Produces warning if it is not.
Produces warning if setup/conda_env.yaml has been altered more recently than the .
Parameters
----------
root : str
Directory of root.
Returns
-------
None
Notes
-----
"""
python_executable = sys.executable
# Check if currently in a conda env
if 'conda' in python_executable:
try:
conda_info = os.path.join(root, '.conda_info')
conda_info_new = os.path.join(root, '.conda_info_new')
if os.path.exists(conda_info):
os.system('conda list --export > %s' % conda_info_new)
if filecmp.cmp(conda_info, conda_info_new):
os.system('rm %s' % conda_info_new)
else:
os.system('rm %s' % conda_info)
os.system('mv %s %s' % (conda_info_new, conda_info))
info_time = os.path.getmtime(conda_info)
info_time = datetime.fromtimestamp(info_time)
conda_yaml = os.path.join(root, 'setup', 'conda_env.yaml')
yaml_time = os.path.getmtime(conda_yaml)
yaml_time = datetime.fromtimestamp(yaml_time)
if yaml_time > info_time:
print(colored(messages.warning_old_conda, 'red'))
else:
os.system('conda list --export > %s' % conda_info)
except:
error_message = 'Error with `check_conda_status`. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()),
None)
else:
print(colored(messages.warning_not_conda, 'red'))
def remove_path(path, option = '', quiet = False):
""".. Remove path using system command.
Remove path ``path`` using system command. Safely removes symbolic links.
Path can be specified with the * shell pattern
(see `here <https://www.gnu.org/software/findutils/manual/html_node/find_html/Shell-Pattern-Matching.html>`__).
Parameters
----------
path : str
Path to remove.
option : str, optional
Options for system command. Defaults to ``-rf`` for POSIX and ``/s /q`` for NT.
quiet : bool, optional
Suppress printing of path removed. Defaults to ``False``.
Returns
-------
None
Example
-------
The following code removes path ``path``.
.. code-block:: python
remove_path('path')
The following code removes all paths beginning with ``path``.
.. code-block:: python
remove_path('path*')
"""
try:
path = norm_path(path)
if not option:
option = metadata.default_options[os.name]['rmdir']
command = metadata.commands[os.name]['rmdir'] % (option, path)
process = subprocess_fix.Popen(command, shell = True)
process.wait()
# ACTION ITEM: ADD DEBUGGING TO SUBPROCESS CALL
if not quiet:
message = 'Removed: `%s`' % path
print(colored(message, metadata.color_success))
except:
error_message = 'Error with `remove_path`. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def end_makelog(paths):
""".. End make log.
Appends to file ``makelog``, recording end time.
Note
----
We allow for writing to a make log even after the make log has ended. We do not recommend this for best practice.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
Path Keys
---------
makelog : str
Path of makelog.
Returns
-------
None
"""
try:
makelog = get_path(paths, 'makelog')
if makelog:
makelog = norm_path(makelog)
message = 'Ending makelog file at: `%s`' % makelog
print(colored(message, metadata.color_success))
if not (metadata.makelog_started and os.path.isfile(makelog)):
raise_from(CritError(messages.crit_error_no_makelog % makelog),
None)
with open(makelog, 'a', encoding='utf8') as MAKELOG:
time_end = str(datetime.datetime.now().replace(microsecond=0))
working_dir = os.getcwd()
print(messages.note_dash_line, file=MAKELOG)
print(messages.note_makelog_end + time_end, file=MAKELOG)
print(messages.note_working_directory + working_dir,
file=MAKELOG)
print(messages.note_dash_line, file=MAKELOG)
except:
error_message = 'Error with `end_makelog`. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def remove_dir(dir_list, quiet = False):
""".. Remove directory using system command.
Remove directories in list ``dir_list`` using system command.
Safely removes symbolic links. Directories can be specified with the * shell pattern
(see `here <https://www.gnu.org/software/findutils/manual/html_node/find_html/Shell-Pattern-Matching.html>`__).
Parameters
----------
dir_list : str, list
Directory or list of directories to remove.
quiet : bool, optional
Suppress printing of directories removed. Defaults to ``False``.
Returns
-------
None
Example
-------
The following code removes directories ``dir1`` and ``dir2``.
.. code-block:: python
remove_dir(['dir1', 'dir2'])
The following code removes directories beginning with ``dir``.
.. code-block:: python
remove_dir(['dir1*'])
"""
try:
dir_list = convert_to_list(dir_list, 'dir')
dir_list = [norm_path(dir_path) for dir_path in dir_list]
dir_list = [d for directory in dir_list for d in glob.glob(directory)]
for dir_path in dir_list:
if os.path.isdir(dir_path):
remove_path(dir_path, quiet = quiet)
elif os.path.isfile(dir_path):
raise_from(TypeError(messages.type_error_not_dir % dir_path), None)
except:
error_message = 'Error with `remove_dir`. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def start_makelog(paths):
""".. Start make log.
Writes file ``makelog``, recording start time. Sets make log status to boolean ``True``, which is used by other functions to confirm make log exists.
Note
----
The make log start condition is used by other functions to confirm a make log exists.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
Path Keys
---------
makelog : str
Path of makelog.
Returns
-------
None
"""
try:
makelog = get_path(paths, 'makelog')
metadata.makelog_started = True
if makelog:
makelog = norm_path(makelog)
message = 'Starting makelog file at: `%s`' % makelog
print(colored(message, metadata.color_success))
with open(makelog, 'w', encoding='utf8') as MAKELOG:
time_start = str(
datetime.datetime.now().replace(microsecond=0))
working_dir = os.getcwd()
print(messages.note_dash_line, file=MAKELOG)
print(messages.note_makelog_start + time_start, file=MAKELOG)
print(messages.note_working_directory + working_dir,
file=MAKELOG)
print(messages.note_dash_line, file=MAKELOG)
except:
error_message = 'Error with `start_makelog`. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def update_internal_paths(paths):
""".. Update within-directory paths using default configuration file.
Returns dictionary ``paths`` with directory locations listed in file ``config``.
Parameters
----------
paths : dict
Dictionary of paths to update.
Dictionary should ex-ante contain values for all keys listed below.
Path Keys
---------
root : str
Path of project repo root
config : str
Path of user configuration file.
Returns
-------
paths : dict
Dictionary of paths.
"""
try:
config_default = get_path(paths, 'config')
config_default = open_yaml(config_default)
root = get_path(paths, 'root')
relative_paths = {path_label: os.path.join(root, path) for \
path_label, path in config_default['make_paths']['root_relative'].items()}
absolute_paths = config_default['make_paths']['absolute']
paths.update(relative_paths)
paths.update(absolute_paths)
return (paths)
except:
error_message = 'Error with update_external_paths. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def update_executables(paths, osname=None):
""".. Update executable names using user configuration file.
Updates executable names with executables listed in file ``config_user``.
Note
----
Executable names are used by :ref:`program functions <program functions>`.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
osname : str, optional
Name of OS. Defaults to ``os.name``.
Path Keys
---------
config_user : str
Path of user configuration file.
Returns
-------
None
"""
osname = osname if osname else os.name # https://github.com/sphinx-doc/sphinx/issues/759
try:
config_user = get_path(paths, 'config_user')
config_user = open_yaml(config_user)
_check_os(osname)
if config_user['local']['executables']:
metadata.default_executables[osname].update(
config_user['local']['executables'])
except:
error_message = 'Error with update_executables. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def update_paths(paths):
""".. Update paths using user configuration file.
Updates dictionary ``paths`` with externals listed in file ``config_user``.
Note
----
The ``paths`` argument for :ref:`sourcing functions<sourcing functions>` is used not only to get
default paths for writing/logging, but also to
`string format <https://docs.python.org/3.4/library/string.html#format-string-syntax>`__
sourcing instructions.
Parameters
----------
paths : dict
Dictionary of paths to update.
Dictionary should ex-ante contain values for all keys listed below.
Path Keys
---------
config_user : str
Path of user configuration file.
Returns
-------
paths : dict
Dictionary of updated paths.
"""
try:
config_user = get_path(paths, 'config_user')
config_user = open_yaml(config_user)
if config_user['external']:
paths.update(config_user['external'])
return (paths)
except:
error_message = 'Error with update_paths. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def unzip(zip_path, output_dir):
""".. Unzip file to directory.
Unzips file ``zip_path`` to directory ``output_dir``.
Parameters
----------
zip_path : str
Path of file to unzip.
output_dir : str
Directory to write outputs of unzipped file.
Returns
-------
None
"""
try:
with zipfile.ZipFile(zip_path, allowZip64=True) as z:
z.extractall(output_dir)
except:
error_message = 'Error with `zip_path`. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def write_source_logs(paths, source_map, depth=float('inf')):
""".. Write source logs.
Logs the following information for sources contained in list ``source_map``
(returned by :ref:`sourcing functions<sourcing functions>`).
- Mapping of symlinks/copies to sources (in file ``source_maplog``)
- Details on files contained in sources:
- File name (in file ``source_statslog``)
- Last modified (in file ``source_statslog``)
- File size (in file ``source_statslog``)
- File head (in file ``source_headlog``, optional)
When walking through sources, float ``depth`` determines level of depth to walk.
Status messages are appended to file ``makelog``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
source_map : list
Mapping of symlinks/copies (destination) to sources (returned by :ref:`sourcing functions<sourcing functions>`).
depth : float, optional
Level of depth when walking through source directories. Defaults to infinite.
Path Keys
---------
source_statslog : str
Path to write source statistics log.
source_headslog : str, optional
Path to write source headers log.
source_maplog : str
Path to write source map log.
makelog : str
Path of makelog.
Returns
-------
None
Example
-------
The following code will log information for all files listed in ``source_map``.
Therefore, files contained in directories listed in ``source_map`` will be ignored.
.. code-block:: python
write_source_logs(paths, depth = 1)
The following code will log information for all files listed in ``source_map``
and any file in all directories listed in ``source_map``, regardless of level of subdirectory.
.. code-block :: python
write_source_logs(paths, depth = float('inf'))
"""
try:
source_statslog = get_path(paths, 'source_statslog')
source_headslog = get_path(paths, 'source_headslog', throw_error=False)
source_maplog = get_path(paths, 'source_maplog')
source_list = [source for source, destination in source_map]
source_list = [glob_recursive(source, depth) for source in source_list]
source_files = [f for source in source_list for f in source]
source_files = set(source_files)
# ACTION: DECIDE WHETHER TO ALLOW FOR RAW DIRECTORY
raw_dir = get_path(paths, 'raw_dir', throw_error=False)
if raw_dir:
raw_files = glob_recursive(raw_dir)
source_files = set(source_files + raw_files)
if source_statslog:
source_statslog = norm_path(source_statslog)
_write_stats_log(source_statslog, source_files)
if source_headslog:
source_headslog = norm_path(source_headslog)
_write_heads_log(source_headslog, source_files)
if source_maplog:
source_maplog = norm_path(source_maplog)
_write_source_maplog(source_maplog, source_map)
message = 'Source logs successfully written!'
write_to_makelog(paths, message)
print(colored(message, metadata.color_success))
except:
error_message = 'Error with `write_source_logs`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def tablefill(inputs, template, output, null='.'):
""".. Fill tables for template using inputs.
Fills tables in document ``template`` using files in list ``inputs``.
Writes filled document to file ``output``.
Null characters in ``inputs`` are replaced with value ``null``.
Parameters
----------
inputs : list
Input or list of inputs to fill into template.
template : str
Path of template to fill.
output : str
Path of output.
null : str
Value to replace null characters (i.e., ``''``, ``'.'``, ``'NA'``). Defaults to ``'.'``.
Returns
-------
None
Example
-------
.. code-block::
#################################################################
# tablefill_readme.txt - Help/Documentation for tablefill.py
#################################################################
Description:
tablefill.py is a Python module designed to fill LyX/Tex tables with output
from text files (usually output from Stata or Matlab).
Usage:
Tablefill takes as input a LyX (or Tex) file containing empty tables (the template
file) and text files containing data to be copied to these tables (the
input files), and produces a LyX (or Tex) file with filled tables (the output file).
For brevity, LyX will be used to denote LyX or Tex files throughout.
Tablefill must first be imported to make.py. This is typically achieved
by including the following lines:
```
from gslab_fill.tablefill import tablefill
```
Once the module has been imported, the syntax used to call tablefill is
as follows:
```
tablefill(input = 'input_file(s)', template = 'template_file',
output = 'output_file')
```
The argument 'template' is the user written LyX file which contains the
tables to be filled in. The argument 'input' is a list of the text files
containing the output to be copied to the LyX tables. If there are multiple
input text files, they are listed as: input = 'input_file_1 input_file_2'.
The argument 'output' is the name of the filled LyX file to be produced.
Note that this file is created by tablefill.py and should not be edited
manually by the user.
###########################
Input File Format:
###########################
The data needs to be tab-delimited rows of numbers (or characters),
preceeded by `<label>`. The < and > are mandatory. The numbers can be
arbitrarily long, can be negative, and can also be in scientific notation.
Examples:
----------
```
<tab:Test>
1 2 3
2 3 1
3 1 2
```
```
<tab:FunnyMat>
1 2 3 23 2
2 3
3 1 2 2
1
```
(The rows do not need to be of equal length.)
Completely blank (no tab) lines are ignored.
If a "cell" is merely "." or "[space]", then it is treated as completely
missing. That is, in the program:
```
<tab:Test>
1 2 3
2 . 1 3
3 1 2
```
is equivalent to:
```
<tab:Test>
1 2 3
2 1 3
3 1 2
```
This feature is useful as Stata outputs missing values in numerical
variables as ".", and missing values in string variables as "[space]".
................................
Scientific Notation Notes:
................................
The scientific notation ihas to be of the form:
[numbers].[numbers]e(+/-)[numbers]
Examples:
```
23.2389e+23
-2.23e-2
-0.922e+3
```
###########################
Template LyX Format:
###########################
The LyX template file determines where the numbers from the input files are placed.
Every table in the template file (if it is to be filled) must appear within a float.
There must be one, and only one, table object inside the float, and the table name
must include a label object that corresponds to the label of the required table in
the input file.
Note that table names cannot be duplicated. For a single template file, each table
to be filled must have a unique label, and there must be one, and only one, table with
that same label in the text files used as input. Having multiple tables with the
same name in the input files or in the template file will cause errors.
Note also that labels are NOT case-sensitive. That is, <TAB:Table1> is considered
the same as `<tab:table1>`.
In the LyX tables, "cells" to be filled with entries from the input text files are
indicated by the following tags:
`"###" (no quotes)`
or
`"#[number][,]#" (no quotes)`
The first case will result in a literal substitution. I.e. whatever is in the text
tables for that cell will be copied over. The second case will convert the data
table's number (if in scientific notation) and will truncate this converted number
to [number] decimal places. It will automatically round while doing so.
If a comma appears after the number (within #[number]#), then it will add commas
to the digits to the left of the decimal place.
Examples:
---------
```
2309.2093 + ### = 2309.2093
2309.2093 + #4# = 2309.2093
2309.2093 + #5# = 2309.20930
2309.2093 + #20# = 2309.20930000000000000000
2309.2093 + #3# = 2309.209
2309.2093 + #2# = 2309.21
2309.2093 + #0# = 2309
2309.2093 + #0,# = 2,309
```
```
-2.23e-2 + #2# = -0.0223 + #2# = -0.02
-2.23e-2 + #7# = -0.0223 + #7# = -0.0223000
-2.23e+10 + #7,# = -22300000000 + #7,# = -22,300,000,000.000000
```
Furthermore, only ###/#num# will be replaced, allowing you to put things around
###/#num# to alter the final output:
Examples:
--------
```
2309.2093 + (#2#) = (2309.21)
2309.2093 + #2#** = 2309.21**
2309.2093 + ab#2#cd = ab2309.21cd
```
If you are doing exact substitution, then you can use characters:
Examples:
---------
`abc + ### = abc`
................................
Intentionally blank cells:
................................
If you would like to display a blank cell, you can use "---":
Examples:
---------
```
--- + ### = ---
--- + #3# = ---
```
######################
# Example Combinations
# Of input + template
######################
Example 1 (Simple)
----------
```
Input: <tab:Test>
1 2 3
2 1 3
3 1 2
Template: `<tab:Test> ` (pretend this is what you see in LyX)
### ### ###
### ### ###
### ### ###
Result:<tab:Test>
1 2 3
2 1 3
3 1 2
```
Example 2 (More Complicated)
----------
```
Input: <tab:Test>
1 . 3
2e-5 1 3.023
. -1 2 3
Template: <tab:Test> (pretend this is what you see in LyX)
(###) 2 ###
#3# ### #1#
NA ### ### ###
Result:<tab:Test>
(1) 2 3
0.000 1 3.0
NA -1 2 3
```
===================
====Important======
===================
By design, missings in input table and "missings" in template do not have to
line up.
Example 3 (LyX)
----------
```
Input: <tab:Test>
1 . 3
2e-5 . 3.023
. -1 2
Template: <tab:Test>
### ### abc
abc #2# #3#
NA ### ###
Result:<tab:Test>
1 3 abc
abc 0.00 3.023
NA -1 2
Recall that to the program, the above input table is no different from:
1 3
2e-5 3.023
-1 2
```
It doesn't "know" where the numbers should be placed within a row, only what
the next number to place should be.
Similarly:
Example 4 (LyX)
----------
```
Input: <tab:Test>
1 1 2
1 1 3
2 -1 2
Template: <tab:Test>
### ### ###
abc abc abc
### #2# #3#
### ### ###
Result:<tab:Test>
1 1 2
abc abc abc
1 1.00 3.000
2 -1 2
```
If a row in the template has no substitutions, then it's not really a row from
the program's point of view.
######################
# Error Logging
######################
If an error occurs during the call to tablefill, it will be displayed in the
command window. When make.py finishes, the user will be able to scroll up
through the output and examine any error messages. Error messages, which
include a description of the error type and a traceback to the line of code
where the error occured, can also be retuned as a string object using the
following syntax:
exitmessage = tablefill( input = 'input_file(s)', template = 'template_file',
output = 'output_file' )
Lines can then be added to make.py to output this string to a log file using
standard Python and built in gslab_make commands.
######################
# Common Errors
######################
Common mistakes which can lead to errors include:
- Mismatch between the length of the LyX table and the corresponding text table.
If the LyX table has more entries to be filled than the text table has entries to
fill from, this will cause an error and the table will not be filled.
- Use of numerical tags (e.g. #1#) to fill non-numerical data. This will cause
an error. Non-numerical data can only be filled using "###", as it does not make
sense to round or truncate this data.
- Multiple table objects in the same float. Each table float in the template LyX
file can only contain one table object. If a float contains a second table object,
this table will not be filled.
######################
# Boldfacing entries
######################
It is straightforward to develop functions that conditionally write entries of
tables in boldface; functions may do so by inserting '\series bold' in the lines
of the filled LyX file immeadiately before phrases that the user wishes to make bold.
"""
try:
inputs = convert_to_list(inputs, 'file')
inputs = [norm_path(file) for file in inputs]
content = [_parse_content(file, null) for file in inputs]
tables = {tag: data for (tag, data) in content}
if (len(content) != len(tables)):
raise_from(CritError(messages.crit_error_duplicate_tables), None)
doc = _insert_tables(template, tables, null)
with io.open(output, 'w', encoding='utf-8') as f:
f.write(doc)
except:
error_message = 'Error with `tablefill`. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def log_files_in_output(paths,
depth = float('inf')):
""".. Log files in output directory.
Logs the following information for all files contained in directory ``output_dir``.
- File name (in file ``output_statslog``)
- Last modified (in file ``output_statslog``)
- File size (in file ``output_statslog``)
- File head (in file ``output_headslog``, optional)
When walking through directory ``output_dir``, float ``depth`` determines level of depth to walk.
Status messages are appended to file ``makelog``.
Include additional output directories to walk through
(typically directories that you wish to keep local) in directory list ``output_local_dir``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
depth : float, optional
Level of depth when walking through output directory. Defaults to infinite.
Path Keys
---------
output_dir : str
Path of output directory.
output_local_dir : str, list, optional
Path or list of paths of local output directories. Defaults to ``[]`` (i.e., none).
output_statslog : str
Path to write output statistics log.
output_headslog : str, optional
Path to write output headers log.
makelog : str
Path of makelog.
Returns
-------
None
Example
-------
The following code will log information for all files contained in
only the first level of ``paths['output_dir']``.
Therefore, files contained in subdirectories will be ignored.
.. code-block:: python
log_files_in_outputs(paths, depth = 1)
The following code will log information for any file in ``paths['output_dir']``,
regardless of level of subdirectory.
.. code-block :: python
log_files_in_outputs(paths, depth = float('inf'))
"""
try:
output_dir = get_path(paths, 'output_dir')
output_local_dir = get_path(paths, 'output_local_dir', throw_error = False)
output_statslog = get_path(paths, 'output_statslog')
output_headslog = get_path(paths, 'output_headslog', throw_error = False)
if output_local_dir:
output_local_dir = convert_to_list(output_local_dir, 'dir')
else:
output_local_dir = []
output_files = glob_recursive(output_dir, depth)
output_local_files = [f for dir_path in output_local_dir for f in glob_recursive(dir_path, depth)]
output_files = set(output_files + output_local_files)
if output_statslog:
output_statslog = norm_path(output_statslog)
_write_stats_log(output_statslog, output_files)
if output_headslog:
output_headslog = norm_path(output_headslog)
_write_heads_log(output_headslog, output_files)
message = 'Output logs successfully written!'
write_to_makelog(paths, message)
print(colored(message, metadata.color_success))
except:
error_message = 'Error with `log_files_in_output`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths, error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def check_module_size(paths):
""".. Check file sizes for module.
Checks file sizes for files to be committed in the current working directory.
Compares file sizes to size limits in file ``config`` and
produces warnings if any of the following limits are exceeded.
- Individual size of a file tracked by git lfs (``file_MB_limit_lfs``)
- Total size of all files tracked by git lfs (``total_MB_limit_lfs``)
- Individual size of a file tracked by git (``file_MB_limit``)
- Total size of all files tracked by git (``total_MB_limit``)
Warning messages are appended to file ``makelog``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
Path Keys
---------
config : str
Path of project configuration file.
makelog : str
Path of makelog.
Returns
-------
None
"""
try:
git_files, git_lfs_files = _get_dir_sizes('.')
file_MB, total_MB, file_MB_lfs, total_MB_lfs = _get_size_values(
git_files, git_lfs_files)
config = get_path(paths, 'config')
config = open_yaml(config)
max_file_sizes = config['max_file_sizes']
print_message = ''
if file_MB > max_file_sizes['file_MB_limit']:
print_message = print_message + messages.warning_git_file_print % max_file_sizes[
'file_MB_limit']
if total_MB > max_file_sizes['total_MB_limit']:
print_message = print_message + messages.warning_git_repo % max_file_sizes[
'total_MB_limit']
if file_MB_lfs > max_file_sizes['file_MB_limit_lfs']:
print_message = print_message + messages.warning_git_lfs_file_print % max_file_sizes[
'file_MB_limit_lfs']
if total_MB_lfs > max_file_sizes['total_MB_limit_lfs']:
print_message = print_message + messages.warning_git_lfs_repo % max_file_sizes[
'total_MB_limit_lfs']
print_message = print_message.strip()
log_message = ''
if file_MB > max_file_sizes['file_MB_limit']:
log_message = log_message + messages.warning_git_file_log % max_file_sizes[
'file_MB_limit']
exceed_files = [
f for (f, s) in git_files.items()
if s / (1024**2) > max_file_sizes['file_MB_limit']
]
exceed_files = '\n'.join(exceed_files)
log_message = log_message + '\n' + exceed_files
if total_MB > max_file_sizes['total_MB_limit']:
log_message = log_message + messages.warning_git_repo % max_file_sizes[
'total_MB_limit']
if file_MB_lfs > max_file_sizes['file_MB_limit_lfs']:
log_message = log_message + messages.warning_git_lfs_file_log % max_file_sizes[
'file_MB_limit_lfs']
exceed_files = [
f for (f, s) in git_lfs_files.items()
if s / (1024**2) > max_file_sizes['file_MB_limit_lfs']
]
exceed_files = '\n'.join(exceed_files)
log_message = log_message + '\n' + exceed_files
if total_MB_lfs > max_file_sizes['total_MB_limit_lfs']:
log_message = log_message + messages.warning_git_lfs_repo % max_file_sizes[
'total_MB_limit_lfs']
log_message = log_message.strip()
if print_message:
print(colored(print_message, metadata.color_failure))
if log_message:
write_to_makelog(paths, log_message)
except:
error_message = 'Error with `check_repo_size`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def execute_command(paths, command, **kwargs):
""".. Run system command.
Runs system command `command` with shell execution boolean ``shell``.
Outputs are appended to file ``makelog`` and written to system command log file ``log``.
Status messages are appended to file ``makelog``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
command : str
System command to run.
shell : `bool`, optional
See `here <https://docs.python.org/3/library/subprocess.html#frequently-used-arguments>`_.
Defaults to ``True``.
log : str, optional
Path of system command log. System command log is only written if specified.
Defaults to ``''`` (i.e., not written).
Path Keys
---------
makelog : str
Path of makelog.
Note
----
We recommend leaving all other parameters to their defaults.
Other Parameters
----------------
osname : str, optional
Name of OS. Used to check if OS is supported. Defaults to ``os.name``.
Returns
-------
None
Example
-------
The following code executes the ``ls`` command,
writes outputs to system command log file ``'file'``,
and appends outputs and/or status messages to ``paths['makelog']``.
.. code-block:: python
execute_command(paths, 'ls', log = 'file')
"""
try:
makelog = get_path(paths, 'makelog')
direct = Directive(makelog=makelog, **kwargs)
# Execute
exit_code, stderr = direct.execute_command(command)
direct.write_log()
if exit_code != 0:
error_message = 'Command executed with errors. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, stderr), None)
except ProgramError:
raise
except:
error_message = 'Error with `execute_command`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def link_inputs(paths, file_list):
""".. Create symlinks to inputs from list of files containing linking instructions.
Create symbolic links using instructions contained in files of list ``file_list``. Instructions are `string formatted <https://docs.python.org/3.4/library/string.html#format-string-syntax>`__ using paths dictionary ``paths``. Symbolic links are written in directory ``input_dir``. Status messages are appended to file ``make log``.
Instruction files on how to create symbolic links (destinations) from targets (sources) should be formatted in the following way.
.. code-block:: md
# Each line of instruction should contain a destination and source delimited by a `|`
# Lines beginning with # are ignored
destination | source
.. Note::
Symbolic links can be created to both files and directories.
.. Note::
Instruction files can be specified with the * shell pattern (see `here <https://www.gnu.org/software/findutils/manual/html_node/find_html/Shell-Pattern-Matching.html>`__). Destinations and their sources can also be specified with the * shell pattern. The number of wildcards must be the same for both destinations and sources.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below. Dictionary additionally used to string format linking instructions.
file_list : str, list
File or list of files containing linking instructions.
Path Keys
---------
input_dir : str
Directory to write symlinks.
makelog : str
Path of makelog.
Returns
-------
source_map : list
List of (source, destination) for each symlink created.
Example
-------
Suppose you call the following function.
.. code-block:: python
link_inputs(paths, ['file1'], formatting_dict)
Suppose ``paths`` contained the following values.
.. code-block:: md
paths = {'root': '/User/root/',
'makelog': 'make.log',
'input_dir': 'input'}
Now suppose instruction file ``file1`` contained the following text.
.. code-block:: md
destination1 | {root}/source1
The ``{root}`` in the instruction file would be string formatted using ``paths``. Therefore, the function would parse the instruction as:
.. code-block:: md
destination1 | /User/root/source1
Example
-------
The following code would use instruction files ``file1`` and ``file2`` to create symbolic links.
.. code-block:: python
link_inputs(paths, ['file1', 'file2'])
Suppose instruction file ``file1`` contained the following text.
.. code-block:: md
destination1 | source1
destination2 | source2
Symbolic links ``destination1`` and ``destination1`` would be created in directory ``paths['input_dir']``. Their targets would be ``source1`` and ``source2``, respectively.
Example
-------
Suppose you have the following targets.
.. code-block:: md
source1
source2
source3
Specifying ``destination* | source*`` in one of your instruction files would create the following symbolic links in ``paths['input_dir']``.
.. code-block:: md
destination1
destination2
destination3
"""
try:
paths['move_dir'] = get_path(paths, 'input_dir')
source_map = _create_links(paths, file_list)
message = 'Input links successfully created!'
write_to_makelog(paths, message)
print(colored(message, metadata.color_success))
return (source_map)
except:
error_message = 'An error was encountered with `link_inputs`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def run_latex(paths, program, **kwargs):
""".. Run LaTeX script using system command.
Compiles document ``program`` using system command, with document specified
in the form of ``script.tex``. Status messages are appended to file ``makelog``.
PDF outputs are written in directory ``output_dir``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
program : str
Path of script to run.
Path Keys
---------
makelog : str
Path of makelog.
output_dir : str
Directory to write PDFs.
Note
----
We recommend leaving all other parameters to their defaults.
Note
----
This function creates and removes a directory named ``latex_auxiliary_dir``.
Other Parameters
----------------
osname : str, optional
Name of OS. Used to determine syntax of system command. Defaults to ``os.name``.
shell : `bool`, optional
See `here <https://docs.python.org/3/library/subprocess.html#frequently-used-arguments>`_.
Defaults to ``True``.
log : str, optional
Path of program log. Program log is only written if specified.
Defaults to ``''`` (i.e., not written).
executable : str, optional
Executable to use for system command.
Defaults to executable specified in :ref:`default settings<default settings>`.
option : str, optional
Options for system command. Defaults to options specified in :ref:`default settings<default settings>`.
args : str, optional
Not applicable.
Returns
-------
None
Example
-------
.. code-block:: python
run_latex(paths, program = 'script.tex')
"""
try:
makelog = get_path(paths, 'makelog')
output_dir = get_path(paths, 'output_dir')
direct = LyXDirective(output_dir=output_dir,
application='latex',
program=program,
makelog=makelog,
**kwargs)
temp_name = direct.program_name
temp_program = direct.program
# Generate folder for auxiliary files
os.mkdir('latex_auxiliary_dir')
# Execute
command = metadata.commands[direct.osname][direct.application] % (
direct.executable, direct.option, temp_program)
exit_code, stderr = direct.execute_command(command)
direct.write_log()
if exit_code != 0:
error_message = 'LaTeX program executed with errors. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, stderr), None)
# Move PDF output
temp_pdf = os.path.join('latex_auxiliary_dir', temp_name + '.pdf')
output_pdf = os.path.join(direct.output_dir,
direct.program_name + '.pdf')
if temp_pdf != output_pdf:
shutil.copy2(temp_pdf, output_pdf)
shutil.rmtree('latex_auxiliary_dir')
# Remove auxiliary files
except ProgramError:
raise
except:
error_message = 'Error with `run_latex`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def run_lyx(paths, program, doctype='', **kwargs):
""".. Run LyX script using system command.
Compiles document ``program`` using system command, with document specified
in the form of ``script.lyx``. Status messages are appended to file ``makelog``.
PDF outputs are written in directory ``output_dir``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
program : str
Path of script to run.
doctype : str, optional
Type of LyX document. Takes either ``'handout'`` and ``'comments'``.
All other strings will default to standard document type.
Defaults to ``''`` (i.e., standard document type).
Path Keys
---------
makelog : str
Path of makelog.
output_dir : str
Directory to write PDFs.
Note
----
We recommend leaving all other parameters to their defaults.
Other Parameters
----------------
osname : str, optional
Name of OS. Used to determine syntax of system command. Defaults to ``os.name``.
shell : `bool`, optional
See `here <https://docs.python.org/3/library/subprocess.html#frequently-used-arguments>`_.
Defaults to ``True``.
log : str, optional
Path of program log. Program log is only written if specified.
Defaults to ``''`` (i.e., not written).
executable : str, optional
Executable to use for system command.
Defaults to executable specified in :ref:`default settings<default settings>`.
option : str, optional
Options for system command. Defaults to options specified in :ref:`default settings<default settings>`.
args : str, optional
Not applicable.
Returns
-------
None
Example
-------
.. code-block:: python
run_lyx(paths, program = 'script.lyx')
"""
try:
makelog = get_path(paths, 'makelog')
output_dir = get_path(paths, 'output_dir')
direct = LyXDirective(output_dir=output_dir,
doctype=doctype,
application='lyx',
program=program,
makelog=makelog,
**kwargs)
# Make handout/comments LyX file
if direct.doctype:
temp_name = os.path.join(direct.program_name + '_' +
direct.doctype)
temp_program = os.path.join(direct.program_dir, temp_name + '.lyx')
beamer = False
shutil.copy2(direct.program, temp_program)
for line in fileinput.input(temp_program,
inplace=True,
backup='.bak'):
if r'\textclass beamer' in line:
beamer = True
if direct.doctype == 'handout' and beamer and (r'\options'
in line):
line = line.rstrip('\n') + ', handout\n'
elif direct.doctype == 'comments' and (
r'\begin_inset Note Note' in line):
line = line.replace('Note Note', 'Note Greyedout')
print(line)
else:
temp_name = direct.program_name
temp_program = direct.program
# Execute
command = metadata.commands[direct.osname][direct.application] % (
direct.executable, direct.option, temp_program)
exit_code, stderr = direct.execute_command(command)
direct.write_log()
if exit_code != 0:
error_message = 'LyX program executed with errors. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, stderr), None)
# Move PDF output
temp_pdf = os.path.join(direct.program_dir, temp_name + '.pdf')
output_pdf = os.path.join(direct.output_dir,
direct.program_name + '.pdf')
if temp_pdf != output_pdf:
shutil.copy2(temp_pdf, output_pdf)
os.remove(temp_pdf)
# Remove handout/comments LyX file
if direct.doctype:
os.remove(temp_program)
except ProgramError:
raise
except:
error_message = 'Error with `run_lyx`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def run_stata(paths, program, **kwargs):
""".. Run Stata script using system command.
Runs script ``program`` using system command, with script specified
in the form of ``script.do``. Status messages are appended to file ``makelog``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
program : str
Path of script to run.
Path Keys
---------
makelog : str
Path of makelog.
Note
----
We recommend leaving all other parameters to their defaults.
Note
----
When a do-file contains a space in its name, different version of Stata save the
corresponding log file with different names. Some versions of Stata truncate the
name to everything before the first space of the do-file name.
Other Parameters
----------------
osname : str, optional
Name of OS. Used to determine syntax of system command. Defaults to ``os.name``.
shell : `bool`, optional
See `here <https://docs.python.org/3/library/subprocess.html#frequently-used-arguments>`_.
Defaults to ``True``.
log : str, optional
Path of program log. Program log is only written if specified.
Defaults to ``''`` (i.e., not written).
executable : str, optional
Executable to use for system command.
Defaults to executable specified in :ref:`default settings<default settings>`.
option : str, optional
Options for system command. Defaults to options specified in :ref:`default settings<default settings>`.
args : str, optional
Not applicable.
Returns
-------
None
Example
-------
.. code-block:: python
run_stata(paths, program = 'script.do')
"""
try:
makelog = get_path(paths, 'makelog')
direct = ProgramDirective(application='stata',
program=program,
makelog=makelog,
**kwargs)
# Get program output (partial)
program_name = direct.program.split(" ")[0]
program_name = os.path.split(program_name)[-1]
program_name = os.path.splitext(program_name)[0]
program_log_partial = os.path.join(os.getcwd(), program_name + '.log')
# Get program output (full)
program_log_full = os.path.join(os.getcwd(),
direct.program_name + '.log')
# Sanitize program
if direct.osname == "posix":
direct.program = re.escape(direct.program)
# Execute
command = metadata.commands[direct.osname]['stata'] % (
direct.executable, direct.option, direct.program)
exit_code, stderr = direct.execute_command(command)
if exit_code != 0:
error_message = 'Stata program executed with errors. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, stderr), None)
try:
output = direct.move_program_output(program_log_partial,
direct.log)
except:
output = direct.move_program_output(program_log_full, direct.log)
_check_stata_output(output)
except ProgramError:
raise
except:
error_message = 'Error with `run_stata`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def run_stat_transfer(paths, program, **kwargs):
""".. Run StatTransfer script using system command.
Runs script ``program`` using system command, with script specified
in the form of ``script.stc`` or ``script.stcmd``.
Status messages are appended to file ``makelog``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
program : str
Path of script to run.
Path Keys
---------
makelog : str
Path of makelog.
Note
----
We recommend leaving all other parameters to their defaults.
Other Parameters
----------------
osname : str, optional
Name of OS. Used to determine syntax of system command. Defaults to ``os.name``.
shell : `bool`, optional
See `here <https://docs.python.org/3/library/subprocess.html#frequently-used-arguments>`_.
Defaults to ``True``.
log : str, optional
Path of program log. Program log is only written if specified.
Defaults to ``''`` (i.e., not written).
executable : str, optional
Executable to use for system command.
Defaults to executable specified in :ref:`default settings<default settings>`.
option : str, optional
Options for system command. Defaults to options specified in :ref:`default settings<default settings>`.
args : str, optional
Not applicable.
Returns
-------
None
Example
-------
.. code-block:: python
run_stat_transfer(paths, program = 'script.stc')
"""
try:
makelog = get_path(paths, 'makelog')
direct = ProgramDirective(application='st',
program=program,
makelog=makelog,
**kwargs)
# Execute
command = metadata.commands[direct.osname][direct.application] % (
direct.executable, direct.program)
exit_code, stderr = direct.execute_command(command)
direct.write_log()
if exit_code != 0:
error_message = 'StatTransfer program executed with errors. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, stderr), None)
except ProgramError:
raise
except:
error_message = 'Error with `run_stat_transfer`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def run_jupyter(paths, program, timeout=None, kernel_name=''):
""".. Run Jupyter notebook using system command.
Runs notebook ``program`` using Python API, with notebook specified
in the form of ``notebook.ipynb``.
Status messages are appended to file ``makelog``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
program : str
Path of script to run.
Path Keys
---------
makelog : str
Path of makelog.
Note
----
We recommend leaving all other parameters to their defaults.
Other Parameters
----------------
timeout : int, optional
Time to wait (in seconds) to finish executing a cell before raising exception.
Defaults to no timeout.
kernel_name : str, optional
Name of kernel to use for execution
(e.g., ``python2`` for standard Python 2 kernel, ``python3`` for standard Python 3 kernel).
Defaults to ``''`` (i.e., kernel specified in notebook).
Returns
-------
None
Example
-------
.. code-block:: python
run_jupyter(paths, program = 'notebook.ipynb')
"""
try:
program = norm_path(program)
with open(program) as f:
message = 'Processing notebook: `%s`' % program
write_to_makelog(paths, message)
print(colored(message, 'cyan'))
if not kernel_name:
kernel_name = 'python%s' % sys.version_info[0]
ep = ExecutePreprocessor(timeout=timeout, kernel_name=kernel_name)
nb = nbformat.read(f, as_version=4)
ep.preprocess(nb, {'metadata': {'path': '.'}})
with open(program, 'wt') as f:
nbformat.write(nb, f)
except:
error_message = 'Error with `run_jupyter`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)