[dev branch] Issues with autometa/config/project.py

[jason-c-kwan]

This file handles configuration handling for the Autometa user project. It contains the definition of the Project class. Here are the issues I found:

1. The docstring for the Project class is not very descriptive and doesn't go into detail about the attributes/properties etc.

2. There is no docstring for the n_metagenomes property in the Project class.

3. There is no docstring for the save method in the Property class.

4. In the add method of the Project class, it basically takes a path to a metagenome config file (supplied through the fpath argument) and is supposed to set up a new directory under the project. However, the first few things that it does is to set up directories and paths that do not use the fpath argument. If the config path it wants to create doesn't exist but the directory that it should be in does:

Autometa/autometa/config/project.py

Lines 117 to 125 in 3e8c771

	metagenome_num = self.new_metagenome_num()
	metagenome_name = f'metagenome_{metagenome_num:03d}'
	metagenome_dirpath = os.path.join(self.dirpath, metagenome_name)
	mg_config_fpath = os.path.join(metagenome_dirpath, f'{metagenome_name}.config')
	# Check presence of metagenome directory and config
	mg_config_present = os.path.exists(mg_config_fpath)
	mg_dir_present = os.path.exists(metagenome_dirpath)
	if not mg_config_present and mg_dir_present:
	raise FileNotFoundError(f'{mg_config_fpath} is not present but the directory exists! Either remove the directory or locate the config file before continuing.')

...then we raise a FileNotFoundError and give a message. However, the message might be confusing to users if the config file they supplied (which has not been used yet), does exist. Perhaps it should be changed to something like "It appears that there is already a metagenome directory as without a config file in the project hierarchy. Please check the integrity of the project file tree."