Skip to content

Commit

Permalink
add codecov badge
Browse files Browse the repository at this point in the history
  • Loading branch information
@rekumar
rekumar authored Dec 24, 2022
1 parent 5f1d7ae commit 29628ec
Showing 1 changed file with 1 addition and 177 deletions.
178 changes: 1 addition & 177 deletions README.md
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rekumar/roboflo/HEAD?labpath=.%2FExamples%2Fbasic%20usage.ipynb)
[![PyPI version](https://badge.fury.io/py/roboflo.svg)](https://badge.fury.io/py/roboflo)
[![codecov](https://codecov.io/gh/rekumar/roboflo/branch/master/graph/badge.svg?token=V3LPNLOJOG)](https://codecov.io/gh/rekumar/roboflo)

![roboflo](/docs/roboflo.png)

Expand All @@ -14,181 +15,4 @@ Happy robot-ing!
![Example Schedule](/docs/exampleschedule.jpg)

PS - shoutout to [Taskpacker](https://github.com/Edinburgh-Genome-Foundry/Taskpacker), from which I drew heavy inspiration. `roboflo` carries much of the design philosophy from `Taskpacker`, but uses only Python packages (the backend is Google ORTools as opposed to Numberjack, which can be difficult to install especially on Windows). `roboflo` also introduces `Transitions`, which define a finite state machine, as a critical component in the workflow under the assumption that many robotic platforms involve workers whose specific jobs are to move things between other workers.
<!--

# Examples
## Solution Mixing
Solutions are defined with the `Solution` class. Solutes and solvents are both defined by their formula, which follows the `(name1)(amount1)_(name2)(amount2)_..._(name)(amount)` format. The names do not have to correspond to elements, so you can use placeholders for units that will be mixed. Parentheses can be used to simplify formulae as well: `A2_B2_C` == `(A_B)2_C`. An `alias` can be provided for the solution to simplify later analysis.
```
stock_solutions = [
Solution(
solutes='FA_Pb_I3',
solvent='DMF9_DMSO1',
molarity=1,
alias='FAPI'
),
Solution(
solutes='MA_Pb_I3',
solvent='DMF9_DMSO1',
molarity=1,
alias='MAPI'
),
]
```
This process goes for both stock and target solutions.
```
densetargets = []
for a in np.linspace(0, 0.8, 5):
densetargets.append(Solution(
solutes=f"FA{a:0.3f}_MA{1-a:.3f}_Pb_I3",
solvent="DMF9_DMSO1",
molarity=1,
alias=f'FA_{a:.3f}'
))
```
Stock and target solutions go into a `Mixer` object
```
sm = Mixer(
stock_solutions = stock_solutions,
targets = {
t:60 #Solution:volume dictionary
for t in densetargets
})
```
which is then solved with constraints
```
sm.solve(
min_volume=20, #minimum volume for a single liquid transfer
max_inputs = 3 #maximum number of solutions that can be mixed to form one target
)
```
The results can be displayed in two ways:
- plain text output of liquid transfers, in order. use of the `alias` term really simplifies this output
```
sm.print()
```
```
===== Stock Prep =====
120.00 of FAPI
180.00 of MAPI
====== Mixing =====
Distribute FAPI:
54.00 to FA_0.600
36.00 to FA_0.400
30.00 to FA_0.800
Distribute MAPI:
60.00 to FA_0.000
36.00 to FA_0.600
54.00 to FA_0.400
30.00 to FA_0.200
Distribute FA_0.600:
30.00 to FA_0.800
Distribute FA_0.400:
30.00 to FA_0.200
```
- a graph of solution transfers. This is harder to use in practice, but can give an overview of the mixing path.
```
fig, ax = plt.subplots(figsize=(6,6))
sm.plot(ax=ax)
```
![Example Mixer.plot()](/docs/example_graph.png)
Note that the units of volume here are arbitrary. Using SI units for small volumes might cause numerical issues when solving a mixture strategy (eg you should use 10 microliters instead of 1e-5 liters).
## Solution Preparation
Mixsol aids in determining the mass of solid reagents needed to form target solutions. We can also check the actual solution formed from recorded reagent masses. Here, the units *do* matter, and you should stick to SI units (mass in grams, volume in liters).
We define solid reagents with the `Powder` class. This requires at least a chemical formula delimited by underscores, similar to the `Solution` definition earlier. If this formula is a proper chemical formula of elements, the molar mass is calculated automatically. If not, you can pass the molar mass directly. The `calculate_molar_mass` function can be used for convenience. `alias` does the same thing it did for `Solution`.
```
from mixsol import Powder, calculate_molar_mass, Weigher
powders = [
Powder('Cs_I'),
Powder('Pb_I2'),
Powder('Pb_Br2'),
Powder('Pb_Cl2'),
Powder(
formula='MA_I',
molar_mass=calculate_molar_mass('C_H6_N_I'),
alias='MAI',
),
Powder(
formula='FA_I',
molar_mass = calculate_molar_mass('C_H5_N2_I'),
alias='FAI',
)
]
```
The list of available `Powder`s is fed into a `Weigher` object
```
weigher = Weigher(
powders=powders
)
```
which can then be used to determine powder amounts for a given volume of a target `Solution`
```
target=Solution(
solutes='Cs0.05_FA0.8_MA0.15_Pb_I2.4_Br0.45_Cl0.15',
solvent='DMF9_DMSO1',
molarity=1
)
answer = weigher.get_weights(
target,
volume=1e-3, #in L
)
print(answer) #masses of each powder, in grams
```
```
{'Cs_I': 0.012990496098, 'Pb_I2': 0.322706258, 'Pb_Br2': 0.082576575, 'Pb_Cl2': 0.020857935, 'MAI': 0.02384543385, 'FAI': 0.1375746568}
```
Finally, we can also generate a `Solution` object by inputting a `{powder:mass}` dictionary into `Weigher`. We will just use the answer from before, but this can be manually input.
```
result = weigher.weights_to_solution(
weights=answer,
volume=1e-3,
solvent='DMF9_DMSO1',
)
print(result)
```
```
2.4M Cs0.0208_I_MA0.0625_FA0.333_Br0.188_Cl0.0625_Pb0.417 in DMF9_DMSO1
```
The molarity of the output will by default be determined by the largest component amount. This can be a bit silly. Passing a component or a numeric value to `norm` can control the molarity. Note that this does not affect the solution itself, just the relative values of the formula units and the overall molarity.
```
result2 = weigher.weights_to_solution(
weights=answer,
volume=1e-3, #in L
solvent='DMF9_DMSO1',
norm='Pb', #normalize the formula+molarity such that Pb=1
)
print(result2) #result is a Solution object
```
```
1.0M Cs0.05_I2.4_Pb_MA0.15_Br0.45_Cl0.15_FA0.8 in DMF9_DMSO1
```
`Solution` objects can be compared - even if their molarity/formulae are apparently different, they will show as equal if the effective molarity of each component is within 0.01% between the solutions.
```
result == result2
```
```
True
```
Read the full documentation [here](https://mixsol.readthedocs.io/en/latest/). -->

0 comments on commit 29628ec

Please sign in to comment.