I think there is a perfect solution to your specific query.
Knowing that there are overlaps of pros and cons (benefits/stunts and benefited by/stunted by) you can easily plan your garden.
I'll give an example of 5 plants :
+2 = Mutual benefits
+1 = Benefited By
0 = No Effect
-1 = Stunted By
-2 = Mutual Stunting
Plant A |+2 B|+1 C | 0 |+1 D|-1 E|-2 |
Plant B |+2 A|+1 | 0 C|+1 E|-1 D|-2 |
Plant C |+2 |+1 A | 0 C|+1 |-1 |-2 E|
Plant D |+2 E|+1 B | 0 |+1 C|-1 |-2 |
Plant E |+2 D|+1 | 0 |+1 B|-1 A|-2 C|
Instead of 10 rows and 100 columns, I'll use a smaller grid of 5 rows and 10 columns to demonstrate a layout
|C|C|A|A|B|B|E|E|D|D| C and E are outside of each others influence [-2]
|C|C|A|A|B|B|E|E|D|D| A and B are paired as they have [+2]
|C|C|A|A|B|B|E|E|D|D| E and D are paired as they have [+2]
|C|C|A|A|B|B|E|E|D|D| B is buffered by E [+1] from D [-1]
|C|C|A|A|B|B|E|E|D|D| C gets no benefit from D [+1]
Should we increase the grid to 12x5 to demonstrate the repetitive pattern, then C does benefit from D [+1]
|C|C|A|A|B|B|E|E|D|D|C|C|.
Note: Your crops are aligned for optimum growth and ease of harvest. The numbers are arbitrary for demonstration purposes as plants also have different requirements such as water, temperature, season, etc.
Should you increase the number of plants and the benefit/stunt variables, you'll be looking at a different chart ;)
Regardless of what the variables are, you will need to group your beds according to the different requirements above, so you already have predefined sets which you are restricted to when formulating your tables.
Hope this helps.
I would like some literature regarding your almanac. Could you point me in the right direction?