Hardcoded paths prevent parallel execution

[aozalevsky]

It would be nice to have the ability to update the PDB-Dev in parallel. Together with the recent updates in #38 it would allow to rebuild the whole repo (with recalculated values) in under 2 minutes on a modern 32-128 core node.

So far I identified several places which interfere with parallel execution:

IHMValidation/master/pyext/src/validation/__init__.py

Lines 737 to 739 in f1aec61

	if os.path.isfile('test.cif'):
	os.remove('test.cif')
	file_re = open('test.cif', 'w')

uses a hardcoded test.cif as a temporary filename

IHMValidation/master/pyext/src/validation/utility.py

Lines 475 to 490 in f1aec61

	def clean_all():
	'''
	delete all generated files
	'''
	# dirname_ed = os.getcwd()
	os.listdir('.')
	for item in os.listdir('.'):
	if item.endswith('.txt'):
	os.remove(item)
	if item.endswith('.csv'):
	os.remove(item)
	if item.endswith('.json'):
	os.remove(item)
	if item.endswith('.sascif'):
	os.remove(item)

removes any temp files by mask, including temp files generated for other structures. It specifically hits sascif processing (looks like other files are not reread again. at least when molprobity and excluded volume are already recalculated).

IHMValidation/master/pyext/src/validation/sas.py

Line 86 in f1aec61

with open(code+'.json', 'w') as f:

IHMValidation/master/pyext/src/validation/sas.py

Line 134 in f1aec61

with open(code+'.sascif', 'w') as f:

IHMValidation/master/pyext/src/validation/sas.py

Lines 370 to 372 in f1aec61

	fname = key+str(fitnum)+'fit.csv'
	with open(fname, 'w') as f:
	f.write(fit.text)

IHMValidation/master/pyext/src/validation/sas.py

Line 379 in f1aec61

fit_1.to_csv('fit1.csv', header=False, index=False)

IHMValidation/master/pyext/src/validation/sas.py

Lines 381 to 382 in f1aec61

	fit_2.to_csv('fit2.csv', header=False, index=False)
	f1 = open('pval.txt', 'w+')

temp files for sas processing.

[aozalevsky]

Fully addressed in v2.0. Keeping open until the merge.