Start by listening to music you like, then pick an instrument. Copy what they did, note by note, but 100x slower. It may not be fun at first, but you will pick up speed slowly, and soon, you're making music, and maybe you'll learn something along the way.
(Okay, technically a song is a pattern. But it's a really nice one.)
Seriously though, you can think of melody and etc as relative parts of a scale as well as intervals between notes. Ear training using scales is simplest and eventually starts to apply to more complicated patterns. Eventually you recognize the intervals and scales even if you are not consciously thinking about the descriptors like 'oh this is a major third interval'
First you familiarize yourself with an interval, by just playing it all over your instrument, listening and singing it.
Then you test your recall: Play a note N, and try to sing N+I (where I is the interval).
Once you know more than one interval, you can also test recognition: Someone else plays an interval (N,N+I) and you try to identify I.
Once you've got the twelve intervals (you can go past the octave but that's pretty easy so basically there are only 12 to learn) you can do similarly for chords. Chords are also easy compared to intervals, though, because they are built up from intervals, so even before you can recognize them all at once, you'll already have the ability to pick them apart note by note to figure out what they are.
If you want to learn improvisation it helps to also investigate "why" - why this particular rhythmic figure (e.g as shown in the OP article), why this chord voicing (e.g. block chords? Quartal harmony? Drop-2?), why this melody (e.g. ascending or descending? Arpeggiating the chords or "playing outside"?) etc etc
Edit: One more thing: it's OK to improvise with the help of something like iReal Pro, but nothing replaces improvising with real humans, find a group of like minded people that would like to play with you
As an aside, music skill (and many other skills) can be divided into Reading and Writing. Reading consists of either actually reading sheet music, or Playing by Ear. Writing is executing what is in your mind. In the context of improvisation, it's coming up with those things to execute in the first place.
To be honest, I am a good Reader, but a poor Writer myself, and still in the beginning of this part of my journey. I love listening to jazz, and playing along, but devising my own melodies is almost beyond the current me. But what's great about music is that every day you practice is one that you get better.
Take the song, load it up in transcribe (https://www.seventhstring.com/) or similar software, pick a part. Up to here, this method and yours is the same. But rather than try to worry about the exact notes being played, study the context by just singing and playing over the song and seeing what works and what does not.
There's just a lot more information than just the notes that were played. So this type of transcription gets you to navigate the same context the musicians were playing in. And as you do it, you'll start hitting the actual notes, and eventually you can close in on them. What's great is that it's fun, playful, musical, and you can do it even with songs that are way out of your level when transcribing note by note or learning from a score.
Using a human language analogy, your suggestion would be to mimic conversations and mine would be to babble in other people's conversations until you become fluent. It's clear in human languages that one is much faster than the other. Sure babies are geared for it, but I think the babbling would work for adults too if they became cute as a baby or puppy, got over themselves, and could shamelessly babble onto other's conversations.
The best book on the matter I've read of how to learn by ear is "The Gift of Music" by Victor Wooten. It's kind of weird in that it's written as a fiction book, but there are definitely music lessons. And if some of them feel too out there, just listen to him play. He's a master, not a stoner pretender.
There's also "Thinking in Jazz", but I am only a fourth or third of the way and so far it's mostly about the historical and cultural background of improvisers. It's not gotten too into the weeds musically speaking.
Do you confirm the name? I cannot find any reference to it. We do have 'The Music Lesson' and 'The Spirit of Music'.
The spirit of music is supposed to be the sequel but I haven't read it yet.
Adults have a hard time learning new things largely because beginner's mind feels so alien and tedious to them. A kid is shocked to discover how great that first E major chord sounds, and experiences like that are motivating.
It's easy for them to find low hanging fruit, because there's so much of it. But if you periodically step back to map the terrain -- how is my rhythm? Can I play to a click? Do I recognize chords as fast as I want? Can I play doublestops? Can I do funk? Counterpoint? Odd time signatures? How are my biomechanics? Bichords (that's two chords at the same time)? Symmetric scales? Microtones (instrument permitting)? Can I do peace? Excitement? Morose? Military? Expansive? Afraid? Call and response between my two hands? Within one hand? -- there's always something within your reach that will feel satisfying when you get it, no matter how much you already know.
Not that you ever necessarily should expect to dominate any of those targets. I will never dominate "rhythm". It's too big. But I'll keep improving.
I wanted something like you describe, but as far as I know nothing existed. So I've been hacking at this and the basic idea does work. It's now just a matter of designing the courses and polishing the user experience.
I am just coming up with the structure for how to define what music would depend on each other. Trying to do it based on music theory would be ideal, but probably beyond my capacity. So I think the historical development of the genre you are trying to learn is a good proxy. For jazz, for example, this would be something like learning African music first, then spirituals, then blues songs, then new orleans jazz, then basic standards and so on. Trane works based on a graph, so the progression does not have to be linear.
It's pretty early stages at the moment. Only one course for now since I've been trying to work out the process first: https://github.com/trane-project/trane-music/blob/master/cou...
These "transcription" courses first ask you to loosely sing the song, then loosely improvise over it with your instruments (you can customize your own), then sing in different keys and do it more thoroughly, then improvise more closely to the actual song. The last step is what is normally called transcribing, but the course is meant to progressively lead you to that. The whole process is meant to recreate the apprenticeship process that all the early Jazz masters went through.
Ideally there's a graphic interface that downloads the music and lets you loop, slow down, and change the pitch. But for now, there's only a command-line interface and the user has to do that themselves. Not ideal, but it works.
Here's one.
Level 1-- learn the bass notes for Heart and Soul
Level 2-- now learn the bass notes in broken thirds
Level 3-- play those bass notes in left hand and root position triads an octave above in right hand
Level 4-- learn to play the melody in the right hand
Level 5-- (big power up needed to continue!) play both l.h. bass notes and r.h. melody
Level 6 Final Boss-- l.h. broken thirds and melody
Now you go through 2nd Quest and play duets with people. It gets fun when you realize it's the same as the A section to I Got Rhythm so jazzers can jump in and noodle around atop your bass patterns.
You can even hear a few of these levels literally in the ending credits to a Tom Hanks movie:
https://www.youtube.com/watch?v=bHwhfJ1zzPs
Good luck and remember to save your game or you'll have to start back at the beginning each time.